Query gi|254780879|ref|YP_003065292.1| hypothetical protein CLIBASIA_03880 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 652 No_of_seqs 232 out of 1214 Neff 7.1 Searched_HMMs 39220 Date Mon May 30 00:49:41 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780879.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK11649 hypothetical protein; 100.0 0 0 670.2 35.6 344 273-639 71-416 (418) 2 COG0739 NlpD Membrane proteins 100.0 1.4E-45 0 339.6 19.0 141 473-616 121-267 (277) 3 PRK10871 nlpD lipoprotein NlpD 100.0 1.5E-43 0 325.3 19.2 119 485-615 254-373 (374) 4 PRK11637 hypothetical protein; 100.0 2E-44 0 331.5 12.0 121 483-610 280-400 (404) 5 pfam01551 Peptidase_M23 Peptid 100.0 2.8E-30 7E-35 231.9 9.7 96 511-608 1-96 (96) 6 COG4942 Membrane-bound metallo 99.9 2.5E-27 6.5E-32 211.1 6.2 128 476-610 289-416 (420) 7 PRK06148 hypothetical protein; 99.5 1.2E-13 3E-18 114.9 8.4 102 510-611 440-553 (1015) 8 PRK06149 hypothetical protein; 98.9 2.8E-09 7.2E-14 84.1 6.8 80 510-603 429-508 (972) 9 pfam04225 OapA Opacity-associa 98.6 6.9E-07 1.8E-11 67.3 10.5 82 276-361 2-83 (85) 10 PRK10783 mltD membrane-bound l 98.1 5.9E-05 1.5E-09 53.7 10.8 108 273-431 340-447 (449) 11 COG3061 OapA Cell envelope opa 98.0 0.00017 4.4E-09 50.5 11.6 83 275-361 158-240 (242) 12 PRK10783 mltD membrane-bound l 97.8 0.00011 2.8E-09 51.8 7.0 122 277-429 264-387 (449) 13 cd00118 LysM Lysin domain, fou 97.6 9.8E-05 2.5E-09 52.2 4.7 45 278-326 2-46 (46) 14 smart00257 LysM Lysin motif. 97.5 0.00012 3E-09 51.6 4.3 44 278-325 1-44 (44) 15 PRK13914 invasion associated s 97.3 0.00055 1.4E-08 46.9 5.1 43 278-325 27-69 (475) 16 pfam01476 LysM LysM domain. Th 97.2 0.00041 1E-08 47.8 4.2 43 279-326 1-43 (43) 17 PRK06347 autolysin; Reviewed 97.0 0.0011 2.9E-08 44.7 4.8 121 275-429 329-449 (593) 18 PRK11198 hypothetical protein; 97.0 0.0023 5.8E-08 42.6 6.0 53 274-326 93-146 (147) 19 PRK06347 autolysin; Reviewed 96.9 0.0079 2E-07 38.7 8.1 123 273-429 402-524 (593) 20 TIGR02899 spore_safA spore coa 96.5 0.002 5.2E-08 42.9 2.6 43 281-326 1-43 (44) 21 TIGR02907 spore_VI_D stage VI 95.6 0.015 3.8E-07 36.8 3.6 70 253-326 301-371 (371) 22 COG1388 LytE FOG: LysM repeat 94.9 0.047 1.2E-06 33.3 4.5 46 277-327 67-112 (124) 23 PRK09439 glucose-specific PTS 94.5 0.12 3.1E-06 30.4 5.9 79 504-585 39-124 (169) 24 cd00210 PTS_IIA_glc PTS_IIA, P 94.4 0.14 3.5E-06 30.0 5.9 77 505-585 18-102 (124) 25 TIGR01843 type_I_hlyD type I s 94.1 0.068 1.7E-06 32.2 3.9 24 42-66 5-28 (434) 26 PRK11649 hypothetical protein; 94.1 0.46 1.2E-05 26.3 9.2 59 271-329 158-216 (418) 27 pfam00358 PTS_EIIA_1 phosphoen 93.7 0.25 6.5E-06 28.1 6.2 78 505-585 23-107 (133) 28 TIGR00830 PTBA PTS system, glu 93.6 0.19 4.8E-06 29.0 5.4 68 514-584 27-109 (129) 29 PRK09824 beta-glucoside-specif 92.3 0.6 1.5E-05 25.5 6.4 79 504-585 495-580 (625) 30 COG1652 XkdP Uncharacterized p 92.1 0.13 3.2E-06 30.3 2.7 50 277-327 211-263 (269) 31 TIGR02013 rpoB DNA-directed RN 91.8 0.41 1E-05 26.7 5.1 162 411-587 658-872 (1449) 32 PRK02597 DNA-directed RNA poly 91.5 0.51 1.3E-05 26.0 5.3 31 551-581 1028-1058(1295) 33 TIGR02005 PTS-IIBC-alpha PTS s 91.2 0.29 7.3E-06 27.8 3.8 67 252-318 409-476 (533) 34 TIGR01995 PTS-II-ABC-beta PTS 91.0 0.46 1.2E-05 26.3 4.7 68 514-584 538-612 (660) 35 PRK10255 N-acetyl glucosamine 90.5 1.2 3.1E-05 23.4 6.5 85 504-591 517-613 (648) 36 COG2190 NagE Phosphotransferas 90.4 1.2 2.9E-05 23.5 6.3 78 505-585 25-109 (156) 37 PRK05305 phosphatidylserine de 89.5 1.4 3.6E-05 22.9 6.2 19 567-585 160-178 (214) 38 CHL00117 rpoC2 RNA polymerase 89.2 1.6 4.1E-05 22.5 6.3 44 531-583 1080-1123(1350) 39 COG4784 Putative Zn-dependent 88.9 1.2 3E-05 23.5 5.3 21 513-533 294-321 (479) 40 pfam01333 Apocytochr_F_C Apocy 87.9 1.3 3.4E-05 23.0 5.1 83 524-612 3-85 (118) 41 TIGR03309 matur_yqeB selenium- 87.4 0.8 2.1E-05 24.6 3.8 19 569-587 179-197 (256) 42 TIGR02971 heterocyst_DevB ABC 87.1 0.55 1.4E-05 25.8 2.8 18 309-326 225-246 (363) 43 CHL00006 consensus 86.6 1.3 3.4E-05 23.1 4.5 57 9-72 307-363 (1372) 44 PRK05258 DNA-directed RNA poly 85.2 2.6 6.7E-05 21.0 5.5 72 508-581 952-1025(1204) 45 TIGR02386 rpoC_TIGR DNA-direct 84.3 2 5.1E-05 21.8 4.5 66 515-581 1324-1394(1552) 46 PRK09603 DNA-directed RNA poly 84.2 2.9 7.4E-05 20.7 6.7 108 521-636 2661-2804(2890) 47 pfam02666 PS_Dcarbxylase Phosp 83.8 3 7.8E-05 20.5 6.3 17 570-586 153-169 (201) 48 PRK00405 rpoB DNA-directed RNA 83.5 1.7 4.3E-05 22.4 3.8 54 521-582 647-719 (1127) 49 PRK06302 acetyl-CoA carboxylas 83.2 0.82 2.1E-05 24.5 2.2 21 569-589 102-122 (155) 50 PRK10260 hypothetical protein; 82.8 3.3 8.5E-05 20.3 5.3 47 277-327 41-89 (306) 51 COG0511 AccB Biotin carboxyl c 80.2 2.4 6E-05 21.3 3.6 57 522-608 69-131 (140) 52 PRK02693 apocytochrome f; Revi 78.8 4.5 0.00011 19.4 4.9 81 523-612 196-279 (312) 53 CHL00001 rpoB RNA polymerase b 77.7 4.8 0.00012 19.2 4.9 57 519-583 566-635 (1065) 54 PRK09890 cold shock protein Cs 76.8 3 7.6E-05 20.6 3.3 47 531-583 6-53 (70) 55 cd06254 M14_ASTE_ASPA_like_4 A 76.1 2.1 5.3E-05 21.7 2.4 19 568-586 237-255 (288) 56 PRK10190 hypothetical protein; 75.3 5.5 0.00014 18.7 4.8 47 277-327 38-86 (310) 57 smart00357 CSP Cold shock prot 75.1 3.2 8.2E-05 20.4 3.1 39 532-575 2-43 (64) 58 pfam00313 CSD 'Cold-shock' DNA 74.8 4.5 0.00011 19.4 3.8 49 531-584 2-50 (66) 59 TIGR02644 Y_phosphoryl pyrimid 74.7 4.6 0.00012 19.3 3.8 57 520-586 338-405 (425) 60 COG3835 CdaR Sugar diacid util 74.6 2.5 6.5E-05 21.1 2.5 14 389-402 327-340 (376) 61 PRK07051 hypothetical protein; 73.3 2.6 6.7E-05 21.0 2.3 18 569-586 26-43 (80) 62 PRK10354 major cold shock prot 73.1 5.2 0.00013 18.9 3.8 33 531-566 6-38 (70) 63 cd06250 M14_PaAOTO_like An unc 72.6 3.2 8.1E-05 20.4 2.6 33 555-587 289-322 (359) 64 cd06255 M14_ASTE_ASPA_like_5 A 72.3 2.9 7.5E-05 20.6 2.4 20 568-587 245-264 (293) 65 LOAD_cold consensus 71.6 6.2 0.00016 18.4 3.9 48 531-584 3-51 (67) 66 cd06252 M14_ASTE_ASPA_like_2 A 71.2 6.9 0.00018 18.1 4.2 21 568-588 258-278 (316) 67 COG3858 Predicted glycosyl hyd 70.8 6.1 0.00016 18.4 3.7 53 275-331 48-100 (423) 68 TIGR01945 rnfC electron transp 70.3 2.1 5.3E-05 21.7 1.2 17 202-218 120-136 (444) 69 cd06251 M14_ASTE_ASPA_like_1 A 70.3 2.8 7.1E-05 20.8 1.9 18 569-586 234-251 (287) 70 cd04458 CSP_CDS Cold-Shock Pro 70.1 6.1 0.00016 18.4 3.6 49 531-584 2-50 (65) 71 cd06253 M14_ASTE_ASPA_like_3 A 69.6 3.7 9.3E-05 20.0 2.3 20 568-587 243-262 (298) 72 PRK10476 multidrug resistance 69.2 7.6 0.00019 17.8 5.6 14 419-432 259-272 (348) 73 PRK05352 Na(+)-translocating N 69.1 3 7.7E-05 20.6 1.8 16 203-218 113-128 (448) 74 COG3170 FimV Tfp pilus assembl 68.9 7.7 0.0002 17.7 7.9 53 276-328 188-248 (755) 75 PRK05820 deoA thymidine phosph 68.2 7.9 0.0002 17.6 3.9 57 520-586 337-404 (440) 76 PRK10943 cold shock-like prote 67.5 6.9 0.00018 18.0 3.4 48 530-583 4-52 (69) 77 PRK04192 V-type ATP synthase s 66.9 7.4 0.00019 17.8 3.5 22 578-599 471-492 (585) 78 cd05830 Sortase_D_5 Sortase D 66.4 4.6 0.00012 19.3 2.3 31 541-575 42-72 (137) 79 pfam09070 PFU PFU (PLAA family 66.3 8.6 0.00022 17.4 3.9 44 543-596 7-50 (115) 80 PRK06078 pyrimidine-nucleoside 66.0 7.6 0.00019 17.8 3.4 57 520-586 332-399 (434) 81 COG3608 Predicted deacylase [G 64.5 9.2 0.00024 17.2 4.8 35 569-606 271-307 (331) 82 COG0187 GyrB Type IIA topoisom 64.5 6 0.00015 18.5 2.6 14 631-644 605-618 (635) 83 CHL00037 petA cytochrome f 64.3 9.3 0.00024 17.1 5.0 81 523-612 203-287 (320) 84 PRK09937 stationary phase/star 64.2 8.8 0.00023 17.3 3.4 48 531-584 3-51 (74) 85 COG1278 CspC Cold shock protei 64.1 6.4 0.00016 18.3 2.7 43 531-576 3-49 (67) 86 pfam00529 HlyD HlyD family sec 64.1 5.1 0.00013 19.0 2.2 26 544-576 278-303 (304) 87 TIGR01349 PDHac_trf_mito pyruv 64.0 6.3 0.00016 18.3 2.7 13 513-525 441-453 (584) 88 PRK09507 cspE cold shock prote 63.8 9.5 0.00024 17.1 3.6 33 531-566 5-37 (69) 89 PRK09578 periplasmic multidrug 63.6 5.4 0.00014 18.8 2.3 14 54-67 12-25 (385) 90 PRK09859 multidrug efflux syst 63.3 5.9 0.00015 18.5 2.4 13 55-67 11-23 (385) 91 pfam05651 Diacid_rec Putative 62.9 5.7 0.00014 18.6 2.2 60 529-589 25-92 (135) 92 cd06850 biotinyl_domain The bi 62.1 5.9 0.00015 18.5 2.2 20 569-588 15-34 (67) 93 PRK05035 electron transport co 62.0 4.9 0.00012 19.1 1.8 14 204-217 131-144 (725) 94 cd06165 Sortase_A_1 Sortase A 60.4 5.8 0.00015 18.6 1.9 56 541-612 39-95 (127) 95 PRK11556 multidrug efflux syst 59.9 7.1 0.00018 17.9 2.3 19 40-63 7-25 (415) 96 PRK10559 p-hydroxybenzoic acid 56.3 13 0.00032 16.2 5.3 14 313-326 201-214 (310) 97 COG1155 NtpA Archaeal/vacuolar 55.8 9.3 0.00024 17.1 2.3 26 281-306 306-331 (588) 98 TIGR01846 type_I_sec_HlyB type 55.7 5.9 0.00015 18.5 1.3 137 277-429 455-595 (703) 99 PRK10218 GTP-binding protein; 54.9 12 0.00031 16.3 2.9 43 545-587 485-530 (607) 100 cd06663 Biotinyl_lipoyl_domain 53.9 9.9 0.00025 16.9 2.2 17 569-585 21-37 (73) 101 pfam00364 Biotin_lipoyl Biotin 53.9 9.9 0.00025 16.9 2.2 18 569-586 21-38 (73) 102 TIGR02472 sucr_P_syn_N sucrose 51.9 5.2 0.00013 18.9 0.5 26 494-532 354-379 (445) 103 cd06166 Sortase_D_5 Sortase D 51.6 9.7 0.00025 17.0 1.9 81 515-611 12-95 (126) 104 pfam02241 MCR_beta Methyl-coen 50.9 13 0.00032 16.2 2.4 46 511-556 155-202 (255) 105 PRK03140 phosphatidylserine de 50.1 16 0.0004 15.5 3.8 35 287-322 35-72 (259) 106 PRK03934 phosphatidylserine de 49.4 7.2 0.00018 17.9 0.9 17 568-584 250-266 (267) 107 TIGR03257 met_CoM_red_bet meth 49.3 13 0.00034 16.0 2.3 51 506-556 334-386 (433) 108 pfam10262 Rdx Rdx family. This 48.9 16 0.00042 15.4 3.7 54 546-609 2-57 (76) 109 cd00004 Sortase Sortases are c 48.8 11 0.00029 16.6 1.8 31 541-575 40-71 (128) 110 KOG3962 consensus 48.8 16 0.00042 15.4 3.7 71 512-588 73-143 (246) 111 cd05828 Sortase_D_4 Sortase D 48.5 10 0.00027 16.8 1.7 14 541-554 41-54 (127) 112 PRK05889 putative acetyl-CoA c 48.1 13 0.00034 16.0 2.1 16 569-584 55-70 (71) 113 pfam10165 Ric8 Guanine nucleot 47.6 6 0.00015 18.5 0.3 84 557-649 337-431 (438) 114 PRK04599 consensus 47.5 14 0.00037 15.8 2.2 32 552-583 251-283 (285) 115 TIGR01394 TypA_BipA GTP-bindin 46.7 17 0.00043 15.3 2.5 199 390-612 326-551 (609) 116 pfam08596 Lgl_C Lethal giant l 46.2 8.2 0.00021 17.5 0.8 142 489-645 224-391 (393) 117 PRK11160 cysteine/glutathione 46.1 15 0.00038 15.7 2.1 15 525-539 543-557 (575) 118 pfam03397 Rhabdo_matrix Rhabdo 45.6 8.1 0.00021 17.6 0.7 47 114-160 16-67 (168) 119 PTZ00265 multidrug resistance 44.7 16 0.00041 15.5 2.1 35 555-591 1172-1210(1467) 120 PRK00044 psd phosphatidylserin 44.4 7 0.00018 18.0 0.2 21 565-585 266-286 (291) 121 TIGR02203 MsbA_lipidA lipid A 44.0 15 0.00037 15.8 1.8 47 281-327 446-497 (603) 122 PRK06823 ornithine cyclodeamin 43.7 16 0.00041 15.5 2.0 14 310-323 205-218 (315) 123 PRK09282 pyruvate carboxylase 43.4 20 0.0005 14.8 4.2 17 522-538 510-526 (580) 124 PRK11892 pyruvate dehydrogenas 43.3 12 0.00029 16.5 1.2 24 93-119 27-50 (464) 125 PRK11174 cysteine/glutathione 43.0 18 0.00045 15.2 2.1 35 524-563 551-585 (588) 126 pfam07831 PYNP_C Pyrimidine nu 42.8 20 0.00051 14.8 2.5 18 569-586 38-55 (75) 127 COG4054 McrB Methyl coenzyme M 41.9 21 0.00053 14.7 2.8 54 504-557 339-394 (447) 128 pfam01887 SAM_adeno_trans S-ad 41.7 21 0.00053 14.7 4.5 22 575-603 220-241 (258) 129 cd06849 lipoyl_domain Lipoyl d 41.7 20 0.00051 14.8 2.2 29 556-584 44-74 (74) 130 PRK10125 predicted glycosyl tr 41.4 10 0.00026 16.9 0.7 40 519-569 326-365 (405) 131 cd05684 S1_DHX8_helicase S1_DH 40.3 17 0.00044 15.2 1.7 48 531-581 5-55 (79) 132 COG4656 RnfC Predicted NADH:ub 40.2 14 0.00036 15.9 1.2 23 278-300 299-321 (529) 133 TIGR01924 rsbW_low_gc anti-sig 39.9 15 0.00039 15.6 1.4 60 285-351 25-85 (161) 134 PRK08225 acetyl-CoA carboxylas 39.7 22 0.00057 14.5 2.2 15 569-583 54-68 (70) 135 TIGR03505 FimV_core FimV N-ter 39.0 23 0.00059 14.4 4.1 43 285-327 1-51 (74) 136 PRK10790 putative multidrug tr 38.9 20 0.00051 14.8 1.9 15 525-539 543-557 (593) 137 COG0845 AcrA Membrane-fusion p 38.5 23 0.0006 14.3 2.2 12 577-588 347-358 (372) 138 COG0213 DeoA Thymidine phospho 37.9 24 0.00061 14.3 3.4 57 520-586 333-400 (435) 139 pfam09449 DUF2020 Domain of un 37.6 24 0.00061 14.2 2.3 24 515-543 76-99 (144) 140 COG4181 Predicted ABC-type tra 37.5 16 0.00041 15.5 1.2 11 279-289 31-41 (228) 141 TIGR01711 gspJ general secreti 37.3 20 0.0005 14.8 1.6 16 442-457 106-121 (202) 142 KOG2525 consensus 36.9 25 0.00063 14.2 3.2 23 514-536 394-416 (496) 143 PRK05559 DNA topoisomerase IV 36.8 25 0.00063 14.1 2.7 11 632-642 607-617 (633) 144 PRK06944 sulfur carrier protei 36.6 7.6 0.00019 17.7 -0.6 49 278-326 9-59 (65) 145 PRK12727 flagellar biosynthesi 36.5 22 0.00056 14.5 1.8 25 286-310 294-318 (557) 146 PRK13657 cyclic beta-1,2-gluca 36.0 25 0.00065 14.1 2.1 52 254-313 335-386 (585) 147 smart00566 consensus 36.0 25 0.00064 14.1 2.0 11 593-603 79-89 (90) 148 PTZ00243 ABC transporter; Prov 35.9 26 0.00065 14.0 2.1 53 554-608 1313-1376(1560) 149 PRK01734 consensus 35.5 14 0.00035 15.9 0.6 34 288-322 49-86 (294) 150 COG1217 TypA Predicted membran 35.3 26 0.00067 14.0 2.7 57 541-611 480-539 (603) 151 pfam11545 HemeBinding_Shp Cell 34.9 26 0.00067 13.9 6.6 97 501-610 13-125 (151) 152 cd03245 ABCC_bacteriocin_expor 34.7 27 0.00068 13.9 2.1 24 278-302 24-47 (220) 153 COG1156 NtpB Archaeal/vacuolar 34.2 27 0.00069 13.9 5.2 29 195-223 148-176 (463) 154 COG0508 AceF Pyruvate/2-oxoglu 33.8 26 0.00066 14.0 1.8 14 616-629 376-389 (404) 155 cd03249 ABC_MTABC3_MDL1_MDL2 M 33.6 28 0.00071 13.8 2.1 14 525-538 206-219 (238) 156 COG1726 NqrA Na+-transporting 33.5 19 0.00049 14.9 1.1 17 62-78 28-44 (447) 157 TIGR00062 L27 ribosomal protei 33.4 28 0.00071 13.8 2.4 30 510-539 43-72 (83) 158 cd03228 ABCC_MRP_Like The MRP 33.2 28 0.00072 13.8 2.2 29 275-304 19-47 (171) 159 TIGR01729 taurine_ABC_bnd taur 32.7 9.7 0.00025 17.0 -0.6 13 399-411 198-210 (304) 160 PRK06549 acetyl-CoA carboxylas 32.6 29 0.00073 13.7 2.2 17 569-585 116-132 (132) 161 PRK10584 putative ABC transpor 32.5 29 0.00074 13.7 2.1 12 524-535 214-225 (228) 162 COG4615 PvdE ABC-type sideroph 32.4 20 0.00051 14.8 1.0 25 278-303 343-367 (546) 163 cd03222 ABC_RNaseL_inhibitor T 32.1 27 0.00068 13.9 1.6 22 281-303 22-43 (177) 164 TIGR01474 ubiA_proteo 4-hydrox 31.6 6.9 0.00017 18.1 -1.5 17 24-41 74-90 (291) 165 TIGR01381 E1_like_apg7 E1-like 31.4 28 0.0007 13.8 1.6 119 440-565 377-516 (689) 166 PTZ00085 40S ribosomal protein 31.3 15 0.00039 15.6 0.3 53 578-632 10-62 (67) 167 PTZ00144 dihydrolipoamide succ 30.8 31 0.00078 13.5 2.1 23 608-631 395-417 (430) 168 COG1912 Uncharacterized conser 30.4 31 0.00079 13.4 1.8 46 558-613 213-259 (268) 169 COG0444 DppD ABC-type dipeptid 29.9 32 0.00081 13.4 2.1 14 421-434 218-231 (316) 170 pfam08710 nsp9 nsp9 replicase. 29.4 32 0.00082 13.3 3.8 33 550-588 76-108 (111) 171 TIGR01348 PDHac_trf_long pyruv 29.2 31 0.0008 13.4 1.6 31 118-153 56-86 (655) 172 TIGR01437 selA_rel pyridoxal p 29.1 16 0.0004 15.5 0.0 22 51-72 66-88 (391) 173 cd03213 ABCG_EPDR ABCG transpo 29.1 33 0.00083 13.3 4.2 47 257-304 7-54 (194) 174 cd00421 intradiol_dioxygenase 28.8 33 0.00084 13.3 1.7 13 592-604 83-95 (146) 175 cd03251 ABCC_MsbA MsbA is an e 28.8 33 0.00084 13.3 2.1 11 526-536 206-216 (234) 176 KOG0215 consensus 28.7 33 0.00084 13.3 4.6 101 539-645 783-912 (1153) 177 KOG1885 consensus 28.6 33 0.00085 13.2 3.2 34 595-633 465-499 (560) 178 TIGR02408 ectoine_ThpD ectoine 28.4 17 0.00044 15.3 0.1 10 394-403 190-199 (278) 179 cd03288 ABCC_SUR2 The SUR doma 28.0 34 0.00087 13.2 2.1 44 256-303 22-65 (257) 180 cd04100 Asp_Lys_Asn_RS_N Asp_L 28.0 34 0.00087 13.2 4.6 70 534-603 2-79 (85) 181 PRK00624 glycine cleavage syst 27.9 34 0.00087 13.2 2.3 19 570-588 40-58 (113) 182 PRK10789 putative multidrug tr 27.6 35 0.00088 13.1 2.1 16 524-539 517-532 (569) 183 PRK12999 pyruvate carboxylase; 27.5 35 0.00089 13.1 2.1 16 569-584 1093-1108(1147) 184 PRK09473 oppD oligopeptide tra 27.4 35 0.00089 13.1 2.1 24 281-304 114-138 (330) 185 PTZ00109 DNA gyrase subunit b; 27.4 35 0.00089 13.1 1.6 19 398-416 624-642 (941) 186 cd03246 ABCC_Protease_Secretio 27.0 35 0.0009 13.0 2.2 30 274-304 18-47 (173) 187 PRK11022 dppD dipeptide transp 26.7 36 0.00091 13.0 2.1 13 422-434 219-231 (327) 188 pfam04203 Sortase Sortase fami 26.6 36 0.00092 13.0 2.4 28 543-575 38-65 (122) 189 pfam04017 DUF366 Domain of unk 26.5 24 0.00061 14.3 0.6 13 313-325 99-111 (183) 190 TIGR00030 S21p ribosomal prote 26.3 36 0.00093 13.0 1.9 18 278-295 2-19 (58) 191 cd02577 PSTD1 PSTD1: Pseudouri 26.1 37 0.00094 12.9 2.2 12 291-302 46-57 (319) 192 COG1038 PycA Pyruvate carboxyl 26.1 31 0.00078 13.5 1.1 23 569-591 1095-1117(1149) 193 PRK07440 hypothetical protein; 26.1 16 0.00041 15.5 -0.4 48 279-326 14-64 (70) 194 cd03247 ABCC_cytochrome_bd The 26.0 37 0.00094 12.9 2.1 29 275-304 19-47 (178) 195 cd00257 Fascin Fascin-like dom 26.0 37 0.00094 12.9 5.1 51 516-566 46-96 (119) 196 pfam06898 YqfD Putative stage 25.8 37 0.00095 12.9 3.4 10 446-455 158-167 (383) 197 COG1566 EmrA Multidrug resista 25.7 37 0.00095 12.9 4.2 21 42-63 16-36 (352) 198 COG0050 TufB GTPases - transla 25.5 33 0.00085 13.2 1.2 30 298-327 186-215 (394) 199 pfam07126 DUF1379 Protein of u 25.5 38 0.00096 12.9 4.4 51 532-584 90-140 (154) 200 COG5526 Lysozyme family protei 25.4 33 0.00084 13.3 1.1 21 409-429 65-85 (191) 201 PRK05644 gyrB DNA gyrase subun 25.3 38 0.00097 12.8 2.2 16 400-415 469-484 (725) 202 TIGR00955 3a01204 Pigment prec 25.3 38 0.00097 12.8 3.2 58 295-357 205-271 (671) 203 cd03812 GT1_CapH_like This fam 25.3 38 0.00097 12.8 2.2 39 518-567 285-323 (358) 204 PRK12835 3-ketosteroid-delta-1 25.2 38 0.00097 12.8 3.4 25 387-411 429-453 (584) 205 PRK11176 lipid transporter ATP 25.2 30 0.00076 13.6 0.9 46 255-304 342-387 (581) 206 PRK07843 3-ketosteroid-delta-1 25.1 38 0.00097 12.8 3.4 34 386-419 418-457 (560) 207 PRK03481 consensus 25.0 38 0.00098 12.8 1.5 36 552-587 253-289 (322) 208 PRK05704 dihydrolipoamide succ 25.0 38 0.00098 12.8 2.2 23 608-631 370-392 (406) 209 cd03369 ABCC_NFT1 Domain 2 of 24.9 39 0.00098 12.8 2.2 44 257-304 10-53 (207) 210 PRK04350 thymidine phosphoryla 24.7 39 0.00099 12.8 4.0 53 520-586 414-474 (502) 211 cd04949 GT1_gtfA_like This fam 24.6 23 0.00059 14.3 0.2 42 518-569 297-339 (372) 212 PRK10419 nikE nickel transport 24.6 39 0.001 12.7 2.1 10 424-433 219-228 (266) 213 cd00728 malate_synt_G Malate s 24.4 9.8 0.00025 17.0 -1.7 23 575-597 523-545 (712) 214 KOG3679 consensus 24.3 8.7 0.00022 17.3 -2.0 45 595-639 566-615 (802) 215 TIGR01172 cysE serine O-acetyl 24.3 40 0.001 12.7 1.6 14 443-456 92-105 (163) 216 PRK12839 hypothetical protein; 24.2 40 0.001 12.7 3.4 24 386-409 428-451 (574) 217 PRK09838 periplasmic copper-bi 24.2 40 0.001 12.7 3.3 27 313-339 84-110 (114) 218 COG1820 NagA N-acetylglucosami 24.1 28 0.00072 13.8 0.6 11 275-285 183-193 (380) 219 PRK08291 ornithine cyclodeamin 24.0 40 0.001 12.7 2.3 15 310-324 210-224 (330) 220 PRK11308 dppF dipeptide transp 23.8 40 0.001 12.7 2.1 11 424-434 222-232 (327) 221 PRK09099 type III secretion sy 23.6 41 0.001 12.6 6.8 26 514-539 317-342 (441) 222 TIGR01936 nqrA NADH:ubiquinone 23.5 25 0.00065 14.1 0.3 24 199-222 108-131 (466) 223 COG4729 Uncharacterized conser 23.5 41 0.001 12.6 2.9 40 571-610 87-131 (156) 224 PRK13546 teichoic acids export 23.4 41 0.001 12.6 2.1 19 290-308 109-127 (264) 225 TIGR00396 leuS_bact leucyl-tRN 23.3 37 0.00093 12.9 1.0 244 272-564 390-666 (916) 226 TIGR00986 3a0801s05tom22 mitoc 23.3 39 0.00099 12.7 1.2 25 52-76 104-128 (152) 227 COG4172 ABC-type uncharacteriz 23.2 41 0.0011 12.6 2.0 19 571-589 306-324 (534) 228 cd00164 S1_like S1_like: Ribos 23.1 42 0.0011 12.6 3.7 45 531-581 2-48 (65) 229 pfam04239 DUF421 Protein of un 23.0 42 0.0011 12.5 4.1 40 278-318 9-48 (98) 230 TIGR02465 chlorocat_1_2 chloro 23.0 40 0.001 12.7 1.2 26 287-312 15-40 (258) 231 pfam08724 Rep_N Rep protein ca 22.9 42 0.0011 12.5 1.3 11 277-287 86-96 (186) 232 PRK03695 vitamin B12-transport 22.5 43 0.0011 12.5 2.2 22 518-539 192-213 (245) 233 pfam08986 DUF1889 Domain of un 22.3 13 0.00034 16.1 -1.4 17 544-561 96-112 (119) 234 TIGR02441 fa_ox_alpha_mit fatt 22.3 43 0.0011 12.4 3.6 34 474-508 659-692 (740) 235 TIGR02645 ARCH_P_rylase putati 22.2 34 0.00086 13.2 0.7 24 289-312 212-235 (499) 236 cd00187 TOP4c DNA Topoisomeras 22.1 35 0.00089 13.1 0.7 32 130-161 132-163 (445) 237 PRK04722 consensus 22.1 44 0.0011 12.4 1.5 33 289-322 38-74 (280) 238 PRK03598 hypothetical protein; 21.8 44 0.0011 12.4 5.7 14 419-432 252-265 (331) 239 cd03795 GT1_like_4 This family 21.4 38 0.00097 12.8 0.8 29 519-547 285-314 (357) 240 cd03689 RF3_II RF3_II: this su 21.2 45 0.0012 12.3 2.4 24 572-595 59-82 (85) 241 pfam05775 AfaD Enterobacteria 21.2 45 0.0012 12.3 2.8 10 315-324 31-40 (136) 242 PRK13635 cbiO cobalt transport 21.2 45 0.0012 12.3 2.1 14 291-304 107-120 (279) 243 PRK11288 araG L-arabinose tran 21.2 45 0.0012 12.3 2.9 15 574-588 275-289 (501) 244 PRK13633 cobalt transporter AT 21.1 45 0.0012 12.3 2.1 25 290-314 111-135 (281) 245 cd03248 ABCC_TAP TAP, the Tran 21.1 45 0.0012 12.3 2.2 29 274-303 30-58 (226) 246 cd03257 ABC_NikE_OppD_transpor 21.0 46 0.0012 12.3 2.1 25 279-304 26-50 (228) 247 TIGR00848 fruA PTS system, fru 20.9 38 0.00096 12.8 0.7 43 286-329 23-65 (133) 248 COG3767 Uncharacterized low-co 20.6 46 0.0012 12.2 3.3 30 46-75 5-35 (95) 249 PRK13636 cbiO cobalt transport 20.6 46 0.0012 12.2 2.1 10 294-303 111-120 (285) 250 TIGR00078 nadC nicotinate-nucl 20.6 46 0.0012 12.2 2.2 13 299-311 107-119 (276) 251 PRK13642 cbiO cobalt transport 20.2 47 0.0012 12.2 2.1 15 291-305 107-121 (277) 252 PRK12837 3-ketosteroid-delta-1 20.2 47 0.0012 12.2 3.4 24 386-409 376-399 (515) 253 PRK05659 sulfur carrier protei 20.1 24 0.00062 14.2 -0.4 46 278-326 9-60 (66) No 1 >PRK11649 hypothetical protein; Provisional Probab=100.00 E-value=0 Score=670.21 Aligned_cols=344 Identities=25% Similarity=0.381 Sum_probs=309.4 Q ss_pred CCCEEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECCCCCCCEEEEEEECCCCCEEEEEE Q ss_conf 64013688417970899999749998999999998540156101699888999972788864058999716883489998 Q gi|254780879|r 273 EFADDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQKDDKFTIVRFSIYHKQKHLLTIA 352 (652) Q Consensus 273 ~~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~~~~~~~~~r~si~~~~~~~~~va 352 (652) +.....++|++||||++||.++|++..++.+++++. .++++|++||.|.+.++..++ +.++.+........+.. T Consensus 71 ~~~~~~y~V~~GDtLs~If~r~Gl~~~dl~~l~~~~---~~L~~LkpGq~l~~~~~~~G~---L~~L~~~~s~~e~~i~~ 144 (418) T PRK11649 71 EAGVHEYVVSTGDTLSSILNQYGIDMSDISQLAAQD---KELRNLKIGQQLSWTLTADGD---LQRLTWEVSRRETRTYD 144 (418) T ss_pred CCCCEEEEECCCCCHHHHHHHCCCCHHHHHHHHHCC---CCHHHCCCCCEEEEEECCCCC---EEEEEEECCCCCEEEEE T ss_conf 777527897899809999988199999999987626---533107999989999899997---58878613765159999 Q ss_pred ECCCCCEEECCCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHCCCCCEEEEEEE Q ss_conf 42788432013332100000122111233454211025666887199989999999973011101210144540688753 Q gi|254780879|r 353 LNDNNEYVLGVEPVKMDINHQMDYMRTSEESPNIYDGIWRATSFNGMNSNLVKLIMRTLASSVNLQEHLKPTDFLETFFS 432 (652) Q Consensus 353 ~~d~g~fv~~~ep~~~~~~~~~~~~~~~~~~~~I~~SLy~aa~~~gip~~ii~~lv~i~a~dVDFqr~ir~GD~f~Vlye 432 (652) +.+.+ |. ........+++.....++|.+|||.++.++|++.++|++++++|+|+||| +++++||+|+|+|+ T Consensus 145 r~~~g-f~-------~~~~~~~~e~~~~~~~G~I~~Sl~~Sa~~aGl~~~~i~~l~~i~~~~IDF-rdlr~GD~F~Vl~e 215 (418) T PRK11649 145 RTANG-FK-------ETSEMQQGEWVNSVLKGTVGGSFVASAKNAGLTSAEISAVIKALQWQMDF-RKLKKGDEFSVLMS 215 (418) T ss_pred ECCCC-CE-------EEEEECCCCCCCCEEEEEECCCHHHHHHHCCCCHHHHHHHHHHHCCCCEE-EECCCCCEEEEEEE T ss_conf 43787-21-------58753056542224799990608999988599989999999984686110-02489987999999 Q ss_pred EECCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCC-CCCCCCCCCCCCC-CCCCCCC Q ss_conf 2115785124672368896238854201345576655444335566100000112333-4541023567641-4340443 Q gi|254780879|r 433 VNHANNQASDDSELLYIHARFGETRTRFYRFLNPVDGSVEYFNENGKSSRPFLLRTPV-PFGRMTSGFGMRY-HPILGYS 510 (652) Q Consensus 433 ~~~~~g~~~~~geil~A~~~~~g~~~~~yrf~~~~~~~~~yyd~~G~S~~k~llr~Pv-~~~risS~Fg~R~-hPilg~~ 510 (652) +.+.+++. ..++|+++.+.++|+++.+|++.+ + .|||++|+|++++|+|+|+ .+.||||+||+|| |||+|++ T Consensus 216 ~~~~dg~~-~~~~ilaa~~~~~gk~~~a~~~~d---g--~yYd~~G~sl~k~flr~P~~~~~RiSS~f~~~R~HPi~g~~ 289 (418) T PRK11649 216 REMLDGKR-EQSQLLGVRLRSGGKDYYAIRAED---G--KFYDRNGTGLAKGFLRFPTAKQFRISSNFNPRRLNPVTGRV 289 (418) T ss_pred EEEECCCC-CCCCEEEEEEECCCEEEEEEECCC---C--CEECCCCHHHHHHHHHCCCCCCCEECCCCCCCCEECCCCCC T ss_conf 99846974-654089999984993799998889---9--86598766388887348666895578999898721778957 Q ss_pred CCCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCC Q ss_conf 46420030267967279715967999653089700799983997488200214454118899788349589984166788 Q gi|254780879|r 511 RMHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLS 590 (652) Q Consensus 511 r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~S 590 (652) +||+|||||||.||||+|++||+|+++||.+||||+|+|+|++||.|.|+|||+|+ |++||+|+|||+||||||||+| T Consensus 290 ~~H~GvD~aap~GTPV~A~~dG~V~~ag~~~~yG~~V~I~H~~~~~T~Y~HLs~~~--V~~Gq~V~~Gq~Ig~vGsTG~s 367 (418) T PRK11649 290 APHRGVDFAMPQGTPVLSVGDGEVVVAKRSGAAGNYVAIRHGRQYTTRYMHLRKLL--VKPGQKVKRGDRIALSGNTGRS 367 (418) T ss_pred CCCCCCCCCCCCCCEEEEECCEEEEEEEECCCCCCEEEEECCCCEEEEEECCCCCC--CCCCCEECCCCEEEEECCCCCC T ss_conf 55367566676899898524879999788189997799981993099961768477--7994999989989802688378 Q ss_pred CCCEEEEEEEECCEECCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 8742688997867883662000788787888999999999999999984 Q gi|254780879|r 591 TGPHLHYELIVNGIKVDSTKVRIPERENLKGDLLQRFAMEKKRINSLLN 639 (652) Q Consensus 591 TGPHLHfEv~vnG~~VdP~~~~lp~~~~l~~~~l~~F~~~~~~id~ll~ 639 (652) |||||||||++||++||||+++||.+++|+++++++|+++...+-+.|. T Consensus 368 TGPHLHyEv~~ng~~vnPl~vklP~~~~l~~~e~~~F~~~~~~~~~~L~ 416 (418) T PRK11649 368 TGPHLHYEVWINQQAVNPLTAKLPRTEGLTGSDRREYLAQVKEVVPQLR 416 (418) T ss_pred CCCEEEEEEEECCEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC T ss_conf 8973389999999795995346889997898999999999999999753 No 2 >COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane] Probab=100.00 E-value=1.4e-45 Score=339.58 Aligned_cols=141 Identities=47% Similarity=0.860 Sum_probs=131.8 Q ss_pred CCCCCCCCHHHCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEEC-CCCCEEEE Q ss_conf 3355661000001123334--54102356764143404434642003026796727971596799965308-97007999 Q gi|254780879|r 473 YFNENGKSSRPFLLRTPVP--FGRMTSGFGMRYHPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWAG-GYGKQTLI 549 (652) Q Consensus 473 yyd~~G~S~~k~llr~Pv~--~~risS~Fg~R~hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~-GyGn~V~I 549 (652) +++..+.+.....+++|++ .++|+|.||+|.||+++..++|+||||++|.||||+|+++|+|+++|+.+ +|||+|+| T Consensus 121 ~~~~~~~~~~~~~~~~p~~~~~~~i~s~fg~r~~p~~~~~~~h~GiD~aa~~gtpV~A~~~G~V~~~~~~~~~yGn~v~i 200 (277) T COG0739 121 AYDVGGKLLELFGLRWPLPNGKGKISSGFGRRIHPVTGRLEPHKGIDIAAPEGTPVYAAADGVVVFAGNGGWGYGNLVII 200 (277) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCEECCCCCCEEEECCCEEEEEECCCCCCCCEEEEE T ss_conf 11335442112000056667786386567765355556546778805026899867851681899970476667708999 Q ss_pred ECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCCCCEEEEEEEECCE---ECCCCEECCCCC Q ss_conf 8399748820021445411889978834958998416678887426889978678---836620007887 Q gi|254780879|r 550 HHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVNGI---KVDSTKVRIPER 616 (652) Q Consensus 550 ~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vnG~---~VdP~~~~lp~~ 616 (652) +|++||+|.|+|||++. |+.||+|++||+||+||+||+||||||||||++||+ ++||+.. |+.. T Consensus 201 ~H~~g~~t~Y~Hl~~~~--V~~G~~V~~G~~Ig~~G~tG~stgphLHfev~~~g~~~~~~~p~~~-l~~~ 267 (277) T COG0739 201 KHGDGYVTVYAHLSSIL--VKEGQKVKAGQVIGYVGSTGRSTGPHLHFEVRKNGKLVPPVNPARY-LPKG 267 (277) T ss_pred ECCCCEEEEEECCCCCC--CCCCCEEECCCEEEECCCCCCCCCCEEEEEEEECCCCCCCCCHHHH-CCCC T ss_conf 74896588996065013--1589788469789972576775797588988758703675785562-2444 No 3 >PRK10871 nlpD lipoprotein NlpD; Provisional Probab=100.00 E-value=1.5e-43 Score=325.28 Aligned_cols=119 Identities=34% Similarity=0.592 Sum_probs=110.5 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEE-CCCCCEEEEECCCCEEEEEHHHH Q ss_conf 11233345410235676414340443464200302679672797159679996530-89700799983997488200214 Q gi|254780879|r 485 LLRTPVPFGRMTSGFGMRYHPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWA-GGYGKQTLIHHGNGYVSSYNHQD 563 (652) Q Consensus 485 llr~Pv~~~risS~Fg~R~hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~-~GyGn~V~I~H~~Gy~T~YaHlS 563 (652) -++||+.+ ++...|+.+... |+||||+++.|+||+|+++|+|+|+|+. .||||+|+|+|+++|.|+|+|++ T Consensus 254 ~W~WP~~G-kVi~~Fs~~~~g-------nkGidia~~~G~pV~Aaa~G~VvyaG~~l~gyGnliiIkH~~~~lsaYahn~ 325 (374) T PRK10871 254 TWRWPTDG-KVIENFGASEGG-------NKGIDIAGSKGQAIIATADGRVVYAGNALRGYGNLIIIKHNDDYLSAYAHND 325 (374) T ss_pred CCCCCCCC-CCCCCCCCCCCC-------CCEEEEECCCCCEEEECCCEEEEEECCCCCCCCEEEEEECCCCCEEEEECCC T ss_conf 34377898-685404777788-------6507985789981785378389992478787762899984998678616766 Q ss_pred HHHHCCCCCCEEECCCEEEEECCCCCCCCCEEEEEEEECCEECCCCEECCCC Q ss_conf 4541188997883495899841667888742688997867883662000788 Q gi|254780879|r 564 AIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVNGIKVDSTKVRIPE 615 (652) Q Consensus 564 ~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vnG~~VdP~~~~lp~ 615 (652) ++. |++||+|++||+||.||+||.++ ||||||||++|++||||+. ||+ T Consensus 326 ~~l--Vkeg~~V~~Gq~Ia~~G~tg~~~-~~LHFEiR~~g~pvdP~~y-LPk 373 (374) T PRK10871 326 TML--VREQQEVKAGQKIATMGSTGTSS-TRLHFEIRYKGKSVNPLRY-LPQ 373 (374) T ss_pred CCC--CCCCCEECCCCEEEEECCCCCCC-CEEEEEEEECCEECCHHHH-CCC T ss_conf 266--78889988999898643789998-3089999779986694897-649 No 4 >PRK11637 hypothetical protein; Provisional Probab=100.00 E-value=2e-44 Score=331.51 Aligned_cols=121 Identities=29% Similarity=0.460 Sum_probs=113.8 Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHH Q ss_conf 00112333454102356764143404434642003026796727971596799965308970079998399748820021 Q gi|254780879|r 483 PFLLRTPVPFGRMTSGFGMRYHPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQ 562 (652) Q Consensus 483 k~llr~Pv~~~risS~Fg~R~hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHl 562 (652) +..+.||+ .|+++++||.++||.+ .|+||||+++.||||+|+.+|+|+|++|.+||||+|+|+|+|||.|.|+|| T Consensus 280 ~G~l~wPv-~G~i~~~fG~~~~~~~----~~~GidI~a~~Gt~V~Av~~G~Vv~a~~~~gyG~~ViIdHG~g~~TlYah~ 354 (404) T PRK11637 280 RGQAFWPV-RGPTLHRYGEQLQGEL----RWKGMVIGASEGTEVKAIADGRVILADWLQGYGLVVVVEHGKGDMSLYGYN 354 (404) T ss_pred CCCCCCCC-CCCCCCCCCCCCCCCC----CCCCEEEECCCCCEEEEECCEEEEEEEECCCCCCEEEEECCCCCEEECCCC T ss_conf 89857687-7770467899999977----758758756999805410176999911408888579998699465715288 Q ss_pred HHHHHCCCCCCEEECCCEEEEECCCCCCCCCEEEEEEEECCEECCCCE Q ss_conf 445411889978834958998416678887426889978678836620 Q gi|254780879|r 563 DAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVNGIKVDSTK 610 (652) Q Consensus 563 S~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vnG~~VdP~~ 610 (652) |++. |++||+|++||+||+||+||.|||||||||||+||+|||||. T Consensus 355 s~l~--v~~Gq~V~~Gq~Ig~vG~tG~s~g~~LhFEir~~g~~vnP~~ 400 (404) T PRK11637 355 QSAL--VSVGAQVRAGQPIALVGSSGGQGRPSLYFEIRRQGQAVNPQP 400 (404) T ss_pred CCCC--CCCCCEECCCCEEEEEECCCCCCCCEEEEEEEECCEEECHHH T ss_conf 9588--899799899996987326899999658999998999847588 No 5 >pfam01551 Peptidase_M23 Peptidase family M23. Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins, for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown. Probab=99.97 E-value=2.8e-30 Score=231.90 Aligned_cols=96 Identities=53% Similarity=0.934 Sum_probs=94.3 Q ss_pred CCCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCC Q ss_conf 46420030267967279715967999653089700799983997488200214454118899788349589984166788 Q gi|254780879|r 511 RMHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLS 590 (652) Q Consensus 511 r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~S 590 (652) |+|+||||+++.|+||+|+.+|+|++++|..+||++|+|+|++||.|.|+||+++. |++||+|++||+||++|++|.+ T Consensus 1 ~~H~GiDi~~~~G~~V~A~~~G~V~~~~~~~~~G~~v~i~h~~g~~~~Y~hl~~~~--V~~G~~V~~G~~IG~~G~sg~~ 78 (96) T pfam01551 1 RFHKGIDIAAPTGTPVYAAADGVVVFAGYLGGYGNLVIIDHGNGYETLYAHLSKIL--VKVGQRVKAGQVIGTVGSTGRS 78 (96) T ss_pred CCCCCEEECCCCCCEEEEEECEEEEEEEECCCCCEEEEEEECCCCEEEECCCEEEE--ECCCCCHHHCCEEEEECCCCCC T ss_conf 93228984658999899623679999898399885999993898769983644677--9589890139999986789998 Q ss_pred CCCEEEEEEEECCEECCC Q ss_conf 874268899786788366 Q gi|254780879|r 591 TGPHLHYELIVNGIKVDS 608 (652) Q Consensus 591 TGPHLHfEv~vnG~~VdP 608 (652) +|||||||||++|++||| T Consensus 79 ~~~hLHfei~~~~~~vdP 96 (96) T pfam01551 79 TGPHLHFEIRKNGKPVDP 96 (96) T ss_pred CCEEEEEEEEECCEECCC T ss_conf 980899999999999877 No 6 >COG4942 Membrane-bound metallopeptidase [Cell division and chromosome partitioning] Probab=99.94 E-value=2.5e-27 Score=211.05 Aligned_cols=128 Identities=30% Similarity=0.465 Sum_probs=112.6 Q ss_pred CCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCE Q ss_conf 56610000011233345410235676414340443464200302679672797159679996530897007999839974 Q gi|254780879|r 476 ENGKSSRPFLLRTPVPFGRMTSGFGMRYHPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGY 555 (652) Q Consensus 476 ~~G~S~~k~llr~Pv~~~risS~Fg~R~hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy 555 (652) ..|-+..+.-+.|||.+ +|.-.||-..-- ...-+|+-|+++.|++|.|.+||+|+||||..|||.+|+|+|++|| T Consensus 289 t~~~~~~~G~l~~PV~G-~il~rFG~~~~g----g~~wkG~vi~a~~Ga~V~A~AdG~VvyA~~l~GYG~vvIldhG~gy 363 (420) T COG4942 289 TGGFGALRGQLAWPVTG-RILRRFGQADGG----GLRWKGMVIGASAGATVKAIADGRVVYADWLRGYGLVVILDHGGGY 363 (420) T ss_pred CCCCCCCCCCCCCCCCC-HHHHHHCCCCCC----CCCCCCEEEECCCCCEEEECCCCEEEECHHHCCCCEEEEEECCCCC T ss_conf 55320025776888787-078773456788----7610675873599982562069569954332567569999748853 Q ss_pred EEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCCCCEEEEEEEECCEECCCCE Q ss_conf 8820021445411889978834958998416678887426889978678836620 Q gi|254780879|r 556 VSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVNGIKVDSTK 610 (652) Q Consensus 556 ~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vnG~~VdP~~ 610 (652) .+.|+||+.+. |++|+.|+.||.||.||++|-..-|-|+||||.||+||||.. T Consensus 364 ~slyg~~~~i~--v~~G~~V~AGepIa~~G~sgg~~~p~LYfEiR~~G~pvnP~p 416 (420) T COG4942 364 HSLYGGNQSIL--VNPGQFVKAGEPIALVGSSGGQGRPALYFEIRRQGQPVNPQP 416 (420) T ss_pred EEEECCCCEEE--ECCCCEEECCCCHHHCCCCCCCCCCCHHHHHHHCCCCCCCHH T ss_conf 78861664221--068977556971532267789998410021460597479512 No 7 >PRK06148 hypothetical protein; Provisional Probab=99.49 E-value=1.2e-13 Score=114.86 Aligned_cols=102 Identities=27% Similarity=0.493 Sum_probs=84.3 Q ss_pred CCCCCCEEECCCCCCCEEECCCCEEEEEEEE---CCCCCEEEEECC--CC--EEEEEHHHHHHH-HCCCCCCEEECCCEE Q ss_conf 3464200302679672797159679996530---897007999839--97--488200214454-118899788349589 Q gi|254780879|r 510 SRMHTGVDWAAPRGTPIVAVGDGIVEKANWA---GGYGKQTLIHHG--NG--YVSSYNHQDAIA-KNIKAGTAVKQGQII 581 (652) Q Consensus 510 ~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~---~GyGn~V~I~H~--~G--y~T~YaHlS~~a-~gV~~G~~V~qGQvI 581 (652) .-.|.|||+=+|.||||+|.-+|+|+.+..+ -+||-.|+++|. +| +.|.|+||+.-. ..+++|++|++||.| T Consensus 440 RTihLGVDl~~p~gT~V~AP~dG~V~~~~n~~~~l~yGg~iiL~h~~~~~~~F~tLyGhl~~~~~~~l~~G~~i~~G~~i 519 (1015) T PRK06148 440 RTVHLGVDLFMPAGTPVYAPLAGTVRSVEIEAVPLGYGGLIALEHEPPGCPPFYTLWGHLAHEAVSRLKPGDRLAAGELV 519 (1015) T ss_pred CEEEEEEEEEECCCCCEECCCCCEEEEEECCCCCCCCCCEEEEEECCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCEE T ss_conf 32654257750699804466586699962476555677548998425888750565235772553126888850467712 Q ss_pred EEECCCCCCCC--CEEEEEEEE--CCEECCCCEE Q ss_conf 98416678887--426889978--6788366200 Q gi|254780879|r 582 GWIGTTGLSTG--PHLHYELIV--NGIKVDSTKV 611 (652) Q Consensus 582 G~vGsTG~STG--PHLHfEv~v--nG~~VdP~~~ 611 (652) |.+|+....-| |||||.+.- .|...|+-.+ T Consensus 520 g~~G~~~~nggw~phlh~Ql~~~~~~~~~~~Pgv 553 (1015) T PRK06148 520 GHMGDAHENGGWAPHLHFQISTDTQLSATEILGV 553 (1015) T ss_pred EECCCCCCCCCCCCCEEEEEEECCCCCCCCCCCC T ss_conf 3426654468877615898851345678889885 No 8 >PRK06149 hypothetical protein; Provisional Probab=98.93 E-value=2.8e-09 Score=84.10 Aligned_cols=80 Identities=20% Similarity=0.191 Sum_probs=68.9 Q ss_pred CCCCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCC Q ss_conf 34642003026796727971596799965308970079998399748820021445411889978834958998416678 Q gi|254780879|r 510 SRMHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGL 589 (652) Q Consensus 510 ~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~ 589 (652) .-.|.|||+=+|.||||+|.-+|+|. ..||.+|.++|+.-..|.|+++.. ++.|++|+.||.||..++.| T Consensus 429 rTvhLGvDl~~pagTpV~AP~~G~V~-----~~~~g~~~l~~~~~~~~L~g~~~~----~~~g~~i~~G~~ig~~~~~g- 498 (972) T PRK06149 429 ATCALGVELWLAAGTAVAAPFAGEIG-----RDGDGRLTLRGDAWELHLTGVEPA----VADGAAVEAGQPLGSASALG- 498 (972) T ss_pred CEEEEEEEEEECCCCEEECCCCCEEE-----ECCCCEEEEECCCEEEEEECCCCC----CCCCCEEECCCCCCCCCCCC- T ss_conf 50430045660799805466576699-----716964898517548998256776----67767520677003366688- Q ss_pred CCCCEEEEEEEECC Q ss_conf 88742688997867 Q gi|254780879|r 590 STGPHLHYELIVNG 603 (652) Q Consensus 590 STGPHLHfEv~vnG 603 (652) ||||.+.-.. T Consensus 499 ----~l~~ql~~~~ 508 (972) T PRK06149 499 ----FLRVQLCPVA 508 (972) T ss_pred ----CEEEEEECCC T ss_conf ----4799972167 No 9 >pfam04225 OapA Opacity-associated protein A LysM-like domain. This family includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonisation, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation. This is a LysM-like domain. Probab=98.61 E-value=6.9e-07 Score=67.30 Aligned_cols=82 Identities=9% Similarity=0.134 Sum_probs=68.3 Q ss_pred EEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECCCCCCCEEEEEEECCCCCEEEEEEECC Q ss_conf 13688417970899999749998999999998540156101699888999972788864058999716883489998427 Q gi|254780879|r 276 DDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQKDDKFTIVRFSIYHKQKHLLTIALND 355 (652) Q Consensus 276 e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~~~~~~~~~r~si~~~~~~~~~va~~d 355 (652) ++.++|++||||+.|++++|++..|+++++++-.....+.+|++||.+++.....+ ++..+.+..+ ...+...+.. T Consensus 2 W~~y~V~~GdTLs~iFr~~~L~~sDv~~~~~~~g~~k~Ls~Lk~Gq~v~~~~n~~G---~l~~L~i~~~-~~~v~f~R~~ 77 (85) T pfam04225 2 WKTYQVPKGDTLMQVFRDNNLPISDVNAMAKVEGADKPLSNIKSGQLVRIKLNAQG---RVDELQIENG-AGSVMFFRQS 77 (85) T ss_pred CEEEEECCCCCHHHHHHHCCCCHHHHHHHHHCCCCCCCHHHCCCCCEEEEEECCCC---CEEEEEEECC-CEEEEEEECC T ss_conf 70678079985999998829998999999861156780544589999999999999---8899998149-9489999818 Q ss_pred CCCEEE Q ss_conf 884320 Q gi|254780879|r 356 NNEYVL 361 (652) Q Consensus 356 ~g~fv~ 361 (652) +|.|.. T Consensus 78 DGsf~r 83 (85) T pfam04225 78 DGSFGR 83 (85) T ss_pred CCCEEE T ss_conf 986452 No 10 >PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional Probab=98.11 E-value=5.9e-05 Score=53.68 Aligned_cols=108 Identities=17% Similarity=0.166 Sum_probs=72.5 Q ss_pred CCCEEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECCCCCCCEEEEEEECCCCCEEEEEE Q ss_conf 64013688417970899999749998999999998540156101699888999972788864058999716883489998 Q gi|254780879|r 273 EFADDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQKDDKFTIVRFSIYHKQKHLLTIA 352 (652) Q Consensus 273 ~~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~~~~~~~~~r~si~~~~~~~~~va 352 (652) ....+.+.||+||||+.|.+++|++..++.++ |+.. .+.|++||.|.|+......... ... T Consensus 340 ~~~~~~y~Vr~GDtL~~IA~ky~vsv~~L~~~----N~L~-~~~L~~Gq~L~Ip~~~~~~~~~------~~~-------- 400 (449) T PRK10783 340 PLNSRSYKVRSGDTLSGIASRLGVSTKDLQQW----NNLR-GSTLKVGQSLTIGAGSSAQRLA------NNS-------- 400 (449) T ss_pred CCCCEEEEECCCCCHHHHHHHHCCCHHHHHHH----CCCC-CCCCCCCCEEEECCCCCCCCCC------CCC-------- T ss_conf 56760588589998999999979799999998----3999-4447899878737887555565------678-------- Q ss_pred ECCCCCEEECCCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHCCCCCEEEEEE Q ss_conf 4278843201333210000012211123345421102566688719998999999997301110121014454068875 Q gi|254780879|r 353 LNDNNEYVLGVEPVKMDINHQMDYMRTSEESPNIYDGIWRATSFNGMNSNLVKLIMRTLASSVNLQEHLKPTDFLETFF 431 (652) Q Consensus 353 ~~d~g~fv~~~ep~~~~~~~~~~~~~~~~~~~~I~~SLy~aa~~~gip~~ii~~lv~i~a~dVDFqr~ir~GD~f~Vly 431 (652) .+. .-...-.||||..|.+++++..-+.+...+ ...+++|+++.+.. T Consensus 401 -----------~~~--------------~Y~Vk~GDTL~~IArry~Vsv~~L~~wN~~-------~~~L~pGQkL~I~v 447 (449) T PRK10783 401 -----------DSI--------------TYRVRKGDSLSSIAKRHGVNIKDVMRWNSD-------TANLQPGDKLTLFV 447 (449) T ss_pred -----------CCE--------------EEEECCCCCHHHHHHHHCCCHHHHHHHCCC-------CCCCCCCCEEEEEE T ss_conf -----------965--------------899899997999999969899999986599-------77878999889984 No 11 >COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane] Probab=98.02 E-value=0.00017 Score=50.45 Aligned_cols=83 Identities=8% Similarity=0.134 Sum_probs=70.7 Q ss_pred CEEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECCCCCCCEEEEEEECCCCCEEEEEEEC Q ss_conf 01368841797089999974999899999999854015610169988899997278886405899971688348999842 Q gi|254780879|r 275 ADDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQKDDKFTIVRFSIYHKQKHLLTIALN 354 (652) Q Consensus 275 ~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~~~~~~~~~r~si~~~~~~~~~va~~ 354 (652) .++.++|.+|+||..++++++++..|+.++++.-..-..+.+|+.||.++|.....| ++..+.+..+.. ++...+- T Consensus 158 ~wqsy~V~~G~TLaQlFRdn~LpitDVnAMakveGagkpLSnlkaGq~Vki~~naqG---~Vt~L~le~~n~-~vlF~RQ 233 (242) T COG3061 158 NWQSYTVPQGKTLAQLFRDNNLPITDVNAMAKVEGAGKPLSNLKAGQKVKISLNAQG---RVTELRLETGNN-QVLFTRQ 233 (242) T ss_pred CCEEEEECCCCCHHHHHHCCCCCHHHHHHHHHHCCCCCCHHHCCCCCEEEEEECCCC---CEEEEEECCCCC-EEEEEEC T ss_conf 651587168765999876069985776787753047870222147777999974766---457899616985-4889972 Q ss_pred CCCCEEE Q ss_conf 7884320 Q gi|254780879|r 355 DNNEYVL 361 (652) Q Consensus 355 d~g~fv~ 361 (652) .+|.|.. T Consensus 234 ~DGSy~r 240 (242) T COG3061 234 SDGSYIR 240 (242) T ss_pred CCCCCCC T ss_conf 7886222 No 12 >PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional Probab=97.76 E-value=0.00011 Score=51.78 Aligned_cols=122 Identities=13% Similarity=0.051 Sum_probs=55.9 Q ss_pred EEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCE--EEEEECCCCCCCEEEEEEECCCCCEEEEEEEC Q ss_conf 3688417970899999749998999999998540156101699888--99997278886405899971688348999842 Q gi|254780879|r 277 DLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEI--LRIGVVQKDDKFTIVRFSIYHKQKHLLTIALN 354 (652) Q Consensus 277 ~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~--L~I~~~~~~~~~~~~r~si~~~~~~~~~va~~ 354 (652) ..|.|..+-.|..+++-.|++.+++.+. |..++-....++.. |.|+...... +. ..+... .++ T Consensus 264 ~~V~v~~~idL~~~A~~agi~~~~l~~L----NP~~~r~~t~p~g~~~lllP~~~~~~---f~-~~l~~~-----~~~-- 328 (449) T PRK10783 264 ARVDLGSPVELAQVADMAGMSLSKLKTF----NAGVKGSTLGPSGPQYVMVPKKHAEQ---LR-ESLASG-----EIA-- 328 (449) T ss_pred EEEECCCCCCHHHHHHHHCCCHHHHHHH----CHHHCCCCCCCCCCCEEECCHHHHHH---HH-HHHHCC-----CHH-- T ss_conf 9994699866999998819799999985----86517787689998568683799999---99-986122-----122-- Q ss_pred CCCCEEECCCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHCCCCCEEEE Q ss_conf 788432013332100000122111233454211025666887199989999999973011101210144540688 Q gi|254780879|r 355 DNNEYVLGVEPVKMDINHQMDYMRTSEESPNIYDGIWRATSFNGMNSNLVKLIMRTLASSVNLQEHLKPTDFLET 429 (652) Q Consensus 355 d~g~fv~~~ep~~~~~~~~~~~~~~~~~~~~I~~SLy~aa~~~gip~~ii~~lv~i~a~dVDFqr~ir~GD~f~V 429 (652) ...+...... .. .........-.++|+..|.+.+++...+.+..++-+ ..++.|..+.| T Consensus 329 -------~~~~~~~~~~-~~--~~~~~y~Vr~GDtL~~IA~ky~vsv~~L~~~N~L~~------~~L~~Gq~L~I 387 (449) T PRK10783 329 -------AVQSTLVADN-TP--LNSRSYKVRSGDTLSGIASRLGVSTKDLQQWNNLRG------STLKVGQSLTI 387 (449) T ss_pred -------HCCCCCCCCC-CC--CCCEEEEECCCCCHHHHHHHHCCCHHHHHHHCCCCC------CCCCCCCEEEE T ss_conf -------2143100112-45--676058858999899999997979999999839994------44789987873 No 13 >cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. Probab=97.60 E-value=9.8e-05 Score=52.16 Aligned_cols=45 Identities=18% Similarity=0.183 Sum_probs=40.4 Q ss_pred EEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEE Q ss_conf 6884179708999997499989999999985401561016998889999 Q gi|254780879|r 278 LIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIG 326 (652) Q Consensus 278 ~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~ 326 (652) .++|++||||++|+.++|++..++.++ |+..+.+.|++||+|.|+ T Consensus 2 ~y~V~~GDTl~~Ia~~~~v~~~~l~~~----N~~~~~~~l~~Gq~l~iP 46 (46) T cd00118 2 TYTVKKGDTLSSIAQRYGISVEELLKL----NGLSDPDNLQVGQKLKIP 46 (46) T ss_pred EEEECCCCCHHHHHHHHCCCHHHHHHH----CCCCCCCCCCCCCEEEEC T ss_conf 479898999999999989679999986----699997716769999609 No 14 >smart00257 LysM Lysin motif. Probab=97.53 E-value=0.00012 Score=51.59 Aligned_cols=44 Identities=20% Similarity=0.252 Sum_probs=39.1 Q ss_pred EEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEE Q ss_conf 688417970899999749998999999998540156101699888999 Q gi|254780879|r 278 LIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRI 325 (652) Q Consensus 278 ~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I 325 (652) .++|++||||++|..+||++..++.++ |+..+.+.|++||+|.| T Consensus 1 ty~V~~GDTl~~IA~~~~v~~~~l~~~----N~~~~~~~l~~Gq~l~I 44 (44) T smart00257 1 TYTVKKGDTLSSIARRYGISVSDLLEL----NNILDPDNLQVGQKLKI 44 (44) T ss_pred CCEECCCCCHHHHHHHHCCCHHHHHHH----CCCCCCCCCCCCCEEEC T ss_conf 908798988999999989689999987----69999772487999859 No 15 >PRK13914 invasion associated secreted endopeptidase; Provisional Probab=97.27 E-value=0.00055 Score=46.91 Aligned_cols=43 Identities=14% Similarity=0.251 Sum_probs=19.5 Q ss_pred EEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEE Q ss_conf 688417970899999749998999999998540156101699888999 Q gi|254780879|r 278 LIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRI 325 (652) Q Consensus 278 ~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I 325 (652) .|+||+||||++|..+||++.+++.++ |++ ..+.|.|||+|.| T Consensus 27 TytVksGDTLW~IA~kygvSVa~Lks~----NnL-~SD~I~pGQkL~V 69 (475) T PRK13914 27 TVVVEAGDTLWGIAQSKGTTVDAIKKA----NNL-TTDKIVPGQKLQV 69 (475) T ss_pred EEEECCCCCHHHHHHHHCCCHHHHHHH----HCC-CCCEEECCCEEEE T ss_conf 889657985899898819889999997----588-7670506877986 No 16 >pfam01476 LysM LysM domain. The LysM (lysin motif) domain is about 40 residues long. It is found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. The structure of this domain is known. Probab=97.24 E-value=0.00041 Score=47.77 Aligned_cols=43 Identities=14% Similarity=0.165 Sum_probs=36.3 Q ss_pred EEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEE Q ss_conf 884179708999997499989999999985401561016998889999 Q gi|254780879|r 279 IPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIG 326 (652) Q Consensus 279 v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~ 326 (652) ++|++||||+.|.+++|++.+++.++ |+. ....|++||.|.|+ T Consensus 1 y~V~~GDtl~~IA~~~~v~~~~i~~~----N~l-~~~~i~~Gq~l~IP 43 (43) T pfam01476 1 YTVKKGDTLSSIAKRYGITVEELAEL----NGL-SSPNLYVGQKLKIP 43 (43) T ss_pred CEECCCCCHHHHHHHHCCCHHHHHHH----HCC-CCCCCCCCCEEECC T ss_conf 98798987999999989689999998----589-99856889998539 No 17 >PRK06347 autolysin; Reviewed Probab=97.03 E-value=0.0011 Score=44.66 Aligned_cols=121 Identities=8% Similarity=0.070 Sum_probs=66.0 Q ss_pred CEEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECCCCCCCEEEEEEECCCCCEEEEEEEC Q ss_conf 01368841797089999974999899999999854015610169988899997278886405899971688348999842 Q gi|254780879|r 275 ADDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQKDDKFTIVRFSIYHKQKHLLTIALN 354 (652) Q Consensus 275 ~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~~~~~~~~~r~si~~~~~~~~~va~~ 354 (652) .-..++|+.||||+.|..+||++....... ++..+ +.|-+||.|.+............ .... ....+ T Consensus 329 as~tYTV~sGDTl~~IA~KyGtSV~~L~sw----N~is~-~~IY~GQ~L~V~~~s~stnt~~s-----~~nt---~~n~n 395 (593) T PRK06347 329 NAKIYTVVKGDSLWRIANNHKVTVANLKAW----NNLKS-DFIYPGQKLKVSAGSTTSNTNTS-----KPST---GTSTS 395 (593) T ss_pred CCCEEEEECCCCHHHHHHCCCCCHHHHHHH----HCCCC-CCEECCCEEEECCCCCCCCCCCC-----CCCC---CCCCC T ss_conf 564589844868888763155148777776----46567-84331767887467666666667-----7764---54445 Q ss_pred CCCCEEECCCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHCCCCCEEEE Q ss_conf 788432013332100000122111233454211025666887199989999999973011101210144540688 Q gi|254780879|r 355 DNNEYVLGVEPVKMDINHQMDYMRTSEESPNIYDGIWRATSFNGMNSNLVKLIMRTLASSVNLQEHLKPTDFLET 429 (652) Q Consensus 355 d~g~fv~~~ep~~~~~~~~~~~~~~~~~~~~I~~SLy~aa~~~gip~~ii~~lv~i~a~dVDFqr~ir~GD~f~V 429 (652) ................-.|+||..+.+++++-+-+..+.++- -|| |.+|..++| T Consensus 396 ---------------~~~tsstTsa~tYTVkSGDTLw~IA~K~g~SV~~LkswNnLs---sd~---IYpGQvLkV 449 (593) T PRK06347 396 ---------------KPSTSTSTNAKVYTVVKGDSLWRIANNNKVTIANLKSWNNLK---SDF---IYPGQKLKV 449 (593) T ss_pred ---------------CCCCCCCCCCEEEEEECCCCHHHHHHHCCCCHHHHHHHCCCC---CCE---EEECCEEEE T ss_conf ---------------567765433127998228758877741595789975440666---766---863307998 No 18 >PRK11198 hypothetical protein; Provisional Probab=96.98 E-value=0.0023 Score=42.56 Aligned_cols=53 Identities=17% Similarity=0.119 Sum_probs=37.3 Q ss_pred CCEEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHC-CCCHHHCCCCCEEEEE Q ss_conf 4013688417970899999749998999999998540-1561016998889999 Q gi|254780879|r 274 FADDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKN-EVRVDQLTKDEILRIG 326 (652) Q Consensus 274 ~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~-~~~~~~Lr~Gq~L~I~ 326 (652) .+.+.++|++||||++|.+++=-+...-.+|.++-+. ..+.+.|.|||.|+|+ T Consensus 93 ~e~~~YtVq~GDTLw~IA~k~YGd~~~~~~I~eANk~~I~nPd~IyPGQvL~IP 146 (147) T PRK11198 93 PESQFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYPGQVLRIP 146 (147) T ss_pred CCCCEEEECCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCEEECC T ss_conf 998578979899799999998398878999999616508995841899988378 No 19 >PRK06347 autolysin; Reviewed Probab=96.88 E-value=0.0079 Score=38.74 Aligned_cols=123 Identities=10% Similarity=0.078 Sum_probs=66.3 Q ss_pred CCCEEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECCCCCCCEEEEEEECCCCCEEEEEE Q ss_conf 64013688417970899999749998999999998540156101699888999972788864058999716883489998 Q gi|254780879|r 273 EFADDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQKDDKFTIVRFSIYHKQKHLLTIA 352 (652) Q Consensus 273 ~~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~~~~~~~~~r~si~~~~~~~~~va 352 (652) ...-+.++|+.||||+.|..++|++..++..+ +++.. +-|.+||.|.+.-............. ...... T Consensus 402 tTsa~tYTVkSGDTLw~IA~K~g~SV~~Lksw----NnLss-d~IYpGQvLkVs~~ssss~snts~~~--t~s~ss---- 470 (593) T PRK06347 402 STNAKVYTVVKGDSLWRIANNNKVTIANLKSW----NNLKS-DFIYPGQKLKVSAGSTTSNTNTSKPS--TNTNTS---- 470 (593) T ss_pred CCCCEEEEEECCCCHHHHHHHCCCCHHHHHHH----CCCCC-CEEEECCEEEECCCCCCCCCCCCCCC--CCCCCC---- T ss_conf 43312799822875887774159578997544----06667-66863307998056556887766655--455433---- Q ss_pred ECCCCCEEECCCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHCCCCCEEEE Q ss_conf 42788432013332100000122111233454211025666887199989999999973011101210144540688 Q gi|254780879|r 353 LNDNNEYVLGVEPVKMDINHQMDYMRTSEESPNIYDGIWRATSFNGMNSNLVKLIMRTLASSVNLQEHLKPTDFLET 429 (652) Q Consensus 353 ~~d~g~fv~~~ep~~~~~~~~~~~~~~~~~~~~I~~SLy~aa~~~gip~~ii~~lv~i~a~dVDFqr~ir~GD~f~V 429 (652) . ...............-.++||..+.++|+.-.-+.. ++.-.-|+ +.+|..++| T Consensus 471 --------------~---~ss~tstsastYTVksGDSLw~IA~K~GtSV~~L~s---wNniksd~---Iy~GQkLkV 524 (593) T PRK06347 471 --------------K---PSTNTNTNAKVYTVAKGDSLWRIANNNKVTIANLKS---WNNLKSDF---IYPGQKLKV 524 (593) T ss_pred --------------C---CCCCCCCCCEEEEECCCCCHHHHHHHCCCCHHHHHH---HHCCCCCC---EEECEEEEE T ss_conf --------------5---566554454069983685378888770841777555---52457773---350407997 No 20 >TIGR02899 spore_safA spore coat assembly protein SafA; InterPro: IPR014248 This entry represents a domain of about 40 residues long which is found in a variety of enzymes involved in bacterial cell wall degradation , and which may have a general peptidoglycan binding function. Proteins containing this domain include SafA of Bacillus subtilis, which is a protein found at the interface of the spore cortex and spore coat, and which is dependent on SpoVID for its localization. This domain is generally found towards the N-terminus of these proteins. The C-terminal region of these proteins are more variable and may contain blocks of 12-residue and 13-residue repeats, tandem LysM domains (IPR002482 from INTERPRO), or an SCP-like domain (IPR014258 from INTERPRO).. Probab=96.46 E-value=0.002 Score=42.88 Aligned_cols=43 Identities=9% Similarity=0.092 Sum_probs=36.9 Q ss_pred ECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEE Q ss_conf 4179708999997499989999999985401561016998889999 Q gi|254780879|r 281 IQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIG 326 (652) Q Consensus 281 VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~ 326 (652) |++||||.+|+.+|||+-+++.++ -..+.+.+-+-||++|.|+ T Consensus 1 Vq~GDtlWkiA~kygV~~~~Li~~---NpQl~nP~~IyPG~ki~IP 43 (44) T TIGR02899 1 VQKGDTLWKIAKKYGVDLDELIQA---NPQLSNPNLIYPGMKIKIP 43 (44) T ss_pred CCCCCHHHHHHHHHCCCHHHHHHH---CCCCCCCCCCCCCCEECCC T ss_conf 998821477787717876788641---6887888834899511078 No 21 >TIGR02907 spore_VI_D stage VI sporulation protein D; InterPro: IPR014256 This entry represents SpoVID, the stage VI sporulation protein D, which is restricted to endospore-forming bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich in glutamic acid. SpoVID is involved in spore coat assembly in the mother cell compartment late in the process of sporulation.. Probab=95.55 E-value=0.015 Score=36.79 Aligned_cols=70 Identities=14% Similarity=0.070 Sum_probs=49.7 Q ss_pred CCCCCCCCCCCCCCCCCCCCC-CCEEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEE Q ss_conf 122334222665445677776-40136884179708999997499989999999985401561016998889999 Q gi|254780879|r 253 KIIEENRTITSPQVLIDKIPE-FADDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIG 326 (652) Q Consensus 253 ~~~~en~t~~~~~~~~~~~~~-~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~ 326 (652) .--+||++-.+.--....--. +..|+..|+.||||.+|+.||-+++..+.++ |++-....+..||.|.|+ T Consensus 301 ~~r~Ena~YLt~lf~~~eeE~FTKlk~civQe~dtle~IA~RY~~S~~qL~r~----N~leSD~~v~~GQlLYIP 371 (371) T TIGR02907 301 KEREENALYLTKLFAKEEEEEFTKLKMCIVQEGDTLETIAERYEVSVSQLLRV----NQLESDEEVNEGQLLYIP 371 (371) T ss_pred CCCCCHHHHHHHHHHCCCCCCCCCEEEEEEECCCCHHHHHHHHCCCHHHHHHH----CCCCCCHHHCCCCEEECC T ss_conf 78760255777875048432100038889852886554540212586887520----365572335175145219 No 22 >COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane] Probab=94.91 E-value=0.047 Score=33.31 Aligned_cols=46 Identities=11% Similarity=0.146 Sum_probs=38.8 Q ss_pred EEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEE Q ss_conf 368841797089999974999899999999854015610169988899997 Q gi|254780879|r 277 DLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGV 327 (652) Q Consensus 277 ~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~ 327 (652) ..++|++||||+.|.+++|++..++.++ +.+.+. .+..||.|.+.. T Consensus 67 ~~~~V~~gdtL~~Ia~~~~~tv~~l~~~----n~l~~~-~i~~gq~l~~~~ 112 (124) T COG1388 67 VTYTVKKGDTLSKIARKYGVTVAELKQL----NNLSSD-KIKVGQKLKLPV 112 (124) T ss_pred CCEEECCCCCHHHHHHHHCCCHHHHHHH----HCCCCC-CCCCCCEEEECC T ss_conf 6146616875788787708889998765----204576-433475166314 No 23 >PRK09439 glucose-specific PTS system component; Provisional Probab=94.52 E-value=0.12 Score=30.40 Aligned_cols=79 Identities=22% Similarity=0.252 Sum_probs=52.7 Q ss_pred CCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEE-------EECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEE Q ss_conf 43404434642003026796727971596799965-------30897007999839974882002144541188997883 Q gi|254780879|r 504 HPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKAN-------WAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVK 576 (652) Q Consensus 504 hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag-------~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~ 576 (652) .|++-..-|-.|+-+- |.+--|+|.-+|+|...- -....|--|.| |= |.-|.=.+=..|-.-|++||+|+ T Consensus 39 D~vFa~k~mGdG~AI~-P~~~~v~AP~~G~V~~vf~T~HAigi~~~~G~eiLI-Hi-GiDTV~L~G~gF~~~v~~Gd~Vk 115 (169) T PRK09439 39 DVVFAEKIVGDGIAIK-PTGNKIVAPVDGTIGKIFETNHAFSIESDSGVELFV-HF-GIDTVELKGEGFKRIAEEGQRVK 115 (169) T ss_pred CHHHHCCCCCCEEEEE-CCCCEEECCCCEEEEEECCCCCEEEEECCCCCEEEE-EE-CCCCEECCCCCEEEEEECCCEEC T ss_conf 7486057824748998-679989918895999977889389999289989999-97-62402338967269992769988 Q ss_pred CCCEEEEEC Q ss_conf 495899841 Q gi|254780879|r 577 QGQIIGWIG 585 (652) Q Consensus 577 qGQvIG~vG 585 (652) +||.+..+- T Consensus 116 ~G~~L~~~D 124 (169) T PRK09439 116 VGDPIIEFD 124 (169) T ss_pred CCCEEEEEC T ss_conf 999999986 No 24 >cd00210 PTS_IIA_glc PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. Probab=94.36 E-value=0.14 Score=29.99 Aligned_cols=77 Identities=18% Similarity=0.209 Sum_probs=54.3 Q ss_pred CCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCC--------CEEEEEHHHHHHHHCCCCCCEEE Q ss_conf 3404434642003026796727971596799965308970079998399--------74882002144541188997883 Q gi|254780879|r 505 PILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGN--------GYVSSYNHQDAIAKNIKAGTAVK 576 (652) Q Consensus 505 Pilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~--------Gy~T~YaHlS~~a~gV~~G~~V~ 576 (652) |++-..-|=.|+-+- |..--|+|.-+|+|...-.. +..+-|+..+ |.-|...+-..|..-|++||+|+ T Consensus 18 ~vFs~~~~G~G~AI~-P~~~~v~AP~~G~V~~v~~T---~HAigi~t~~G~evLiHiGiDTV~L~G~gF~~~v~~Gd~V~ 93 (124) T cd00210 18 EVFASKMMGDGFAIK-PSDGKVVAPVDGTIVQIFPT---KHAIGIESDSGVEILIHIGIDTVKLNGEGFTSHVEEGQRVK 93 (124) T ss_pred HHHCCCCCCCEEEEE-CCCCEEECCCCEEEEEECCC---CCEEEEEECCCCEEEEEEEECCCCCCCCCEEEEECCCCEEC T ss_conf 587568822769998-47998990789799998678---96999996899899999730420148953189974889998 Q ss_pred CCCEEEEEC Q ss_conf 495899841 Q gi|254780879|r 577 QGQIIGWIG 585 (652) Q Consensus 577 qGQvIG~vG 585 (652) +||.+..+= T Consensus 94 ~G~~L~~~D 102 (124) T cd00210 94 QGDKLLEFD 102 (124) T ss_pred CCCEEEEEC T ss_conf 999999985 No 25 >TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family; InterPro: IPR010129 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). Type I secretion is an ABC transporter that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C terminus of the transported protein. This entry represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This entry selects a group of sequences closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.; GO: 0015031 protein transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane. Probab=94.15 E-value=0.068 Score=32.15 Aligned_cols=24 Identities=21% Similarity=0.057 Sum_probs=15.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 9989899999999999999987626 Q gi|254780879|r 42 WLSTTFFAGITSGVIIGGSLLTALD 66 (652) Q Consensus 42 w~~~t~ltg~~~~~l~g~a~~~ald 66 (652) ||.--++.++|-+++ +-|.|+-|| T Consensus 5 r~~~~~~~~~v~~~~-~WA~~~~ld 28 (434) T TIGR01843 5 RLITWLIALLVVIFL-LWAAFAPLD 28 (434) T ss_pred HHHHHHHHHHHHHHH-HHHHHHHHC T ss_conf 988999999999999-988876102 No 26 >PRK11649 hypothetical protein; Provisional Probab=94.11 E-value=0.46 Score=26.30 Aligned_cols=59 Identities=14% Similarity=0.245 Sum_probs=49.3 Q ss_pred CCCCCEEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECC Q ss_conf 77640136884179708999997499989999999985401561016998889999727 Q gi|254780879|r 271 IPEFADDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQ 329 (652) Q Consensus 271 ~~~~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~ 329 (652) ..+|.+..+.-.=..+|+..+.++|++..++.+++..|.-..+.+.|+.|+.+.+.++. T Consensus 158 ~~e~~~~~~~G~I~~Sl~~Sa~~aGl~~~~i~~l~~i~~~~IDFrdlr~GD~F~Vl~e~ 216 (418) T PRK11649 158 QGEWVNSVLKGTVGGSFVASAKNAGLTSAEISAVIKALQWQMDFRKLKKGDEFSVLMSR 216 (418) T ss_pred CCCCCCCEEEEEECCCHHHHHHHCCCCHHHHHHHHHHHCCCCEEEECCCCCEEEEEEEE T ss_conf 56542224799990608999988599989999999984686110024899879999999 No 27 >pfam00358 PTS_EIIA_1 phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1. Probab=93.69 E-value=0.25 Score=28.13 Aligned_cols=78 Identities=22% Similarity=0.263 Sum_probs=51.4 Q ss_pred CCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEE-------CCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEEC Q ss_conf 340443464200302679672797159679996530-------8970079998399748820021445411889978834 Q gi|254780879|r 505 PILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWA-------GGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQ 577 (652) Q Consensus 505 Pilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~-------~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~q 577 (652) |++-..-|=.|+-+- |..--|+|.-+|+|...-.. .-.|--|.| |= |.-|.=.+=..|..-|++||+|++ T Consensus 23 ~vFs~~~~G~G~AI~-P~~~~v~AP~~G~V~~v~~T~HAigi~~~~G~eiLi-Hi-GiDTV~L~G~gF~~~v~~Gd~V~~ 99 (133) T pfam00358 23 QVFASKMMGDGFAIK-PSDGKVVAPVDGTIVQIFPTKHAIGIESDGGVEILI-HV-GIDTVKLNGEGFESHVEEGDRVKQ 99 (133) T ss_pred HHHCCCCCCCEEEEE-CCCCEEEECCCEEEEEECCCCCEEEEEECCCCEEEE-EE-CCCCEECCCCCEEEEECCCCEECC T ss_conf 476568822769998-479979907897999986899799999689989999-98-645223389631899758999989 Q ss_pred CCEEEEEC Q ss_conf 95899841 Q gi|254780879|r 578 GQIIGWIG 585 (652) Q Consensus 578 GQvIG~vG 585 (652) ||.|..+= T Consensus 100 G~~L~~~D 107 (133) T pfam00358 100 GDKLLEFD 107 (133) T ss_pred CCEEEEEC T ss_conf 99999985 No 28 >TIGR00830 PTBA PTS system, glucose subfamily, IIA component; InterPro: IPR001127 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) , is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC . These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose , , , . ; GO: 0005351 sugar:hydrogen ion symporter activity, 0006810 transport, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016020 membrane. Probab=93.65 E-value=0.19 Score=29.04 Aligned_cols=68 Identities=24% Similarity=0.314 Sum_probs=53.8 Q ss_pred CCEEECCCCCCCEEECCCC--EEEEE-------EEECCCCCEEEEECCCCEEEEEHHHHH------HHHCCCCCCEEECC Q ss_conf 2003026796727971596--79996-------530897007999839974882002144------54118899788349 Q gi|254780879|r 514 TGVDWAAPRGTPIVAVGDG--IVEKA-------NWAGGYGKQTLIHHGNGYVSSYNHQDA------IAKNIKAGTAVKQG 578 (652) Q Consensus 514 ~GVD~aAp~GTPI~Aag~G--~V~~a-------g~~~GyGn~V~I~H~~Gy~T~YaHlS~------~a~gV~~G~~V~qG 578 (652) +|+=+ -|..=-++|..|| +|..+ |=.+--|--|.| |= |.-|.=..=.. |-.-|++||+|+|| T Consensus 27 dG~AI-~P~~g~v~AP~dGGv~i~~~F~T~HA~gi~s~~G~EiLi-H~-GIDTV~L~G~GPGELEvF~~~v~~G~~V~~G 103 (129) T TIGR00830 27 DGFAI-LPTDGEVVAPVDGGVKITKIFPTKHAIGIESDSGVEILI-HI-GIDTVKLNGEGPGELEVFTSHVEEGDKVKKG 103 (129) T ss_pred CCEEE-ECCCCCEECCCCCCEEEEEECCCCCEEEEEECCCEEEEE-EC-CCCEEEECCCCCCEEEEEEEEEEECCEECCC T ss_conf 86787-408981782421652898973898479998289839999-82-4235887874896131247876438787179 Q ss_pred CEEEEE Q ss_conf 589984 Q gi|254780879|r 579 QIIGWI 584 (652) Q Consensus 579 QvIG~v 584 (652) |.|..+ T Consensus 104 d~l~ef 109 (129) T TIGR00830 104 DPLLEF 109 (129) T ss_pred CEEEEE T ss_conf 779995 No 29 >PRK09824 beta-glucoside-specific PTS system components IIABC; Provisional Probab=92.27 E-value=0.6 Score=25.49 Aligned_cols=79 Identities=14% Similarity=0.169 Sum_probs=55.6 Q ss_pred CCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEE-------EEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEE Q ss_conf 4340443464200302679672797159679996-------530897007999839974882002144541188997883 Q gi|254780879|r 504 HPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKA-------NWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVK 576 (652) Q Consensus 504 hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~a-------g~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~ 576 (652) +|++-..-|-+|+-+- |.---|+|.-||+|... |-.+..|--+.| |= |..|.=.+=..|..-|++||+|+ T Consensus 495 D~~Fa~~~~G~g~ai~-p~~g~v~aP~~g~v~~~~~t~HAig~~~~~G~e~li-Hi-GidTV~l~G~~F~~~v~~g~~V~ 571 (625) T PRK09824 495 DTTFASGLLGKGIAIL-PSVGEVRSPVAGRIASLFATLHAIGIESDDGVEILI-HV-GIDTVKLDGKFFSAHVNVGDKVN 571 (625) T ss_pred CHHHCCCCCCCCEEEE-CCCCEEECCCCCEEEEECCCCCEEEEECCCCCEEEE-EE-CCCCCCCCCCCCEEEECCCCEEC T ss_conf 6554036777966995-699969807980898974789678997289818999-96-61650108915416746789967 Q ss_pred CCCEEEEEC Q ss_conf 495899841 Q gi|254780879|r 577 QGQIIGWIG 585 (652) Q Consensus 577 qGQvIG~vG 585 (652) +||.+...- T Consensus 572 ~g~~l~~~d 580 (625) T PRK09824 572 TGDRLISFD 580 (625) T ss_pred CCCEEEEEC T ss_conf 999899974 No 30 >COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown] Probab=92.06 E-value=0.13 Score=30.29 Aligned_cols=50 Identities=22% Similarity=0.254 Sum_probs=38.3 Q ss_pred EEEEECCCCCHHHHHHHC-CCCHHHHHHHHHHHHC--CCCHHHCCCCCEEEEEE Q ss_conf 368841797089999974-9998999999998540--15610169988899997 Q gi|254780879|r 277 DLIPIQHNTTIFDAMVHA-GYSNGDSAKIAKALKN--EVRVDQLTKDEILRIGV 327 (652) Q Consensus 277 ~~v~VK~GDTL~~IL~r~-Gvs~~ei~~i~~al~~--~~~~~~Lr~Gq~L~I~~ 327 (652) ..++|++||||+.|.++. |... +-..|..+.+. ..+.+.|.+||.|+|+- T Consensus 211 ~~~~v~rgDTl~~is~~~Yg~~~-~y~~I~~aNk~~~~~~pd~I~pGq~l~iP~ 263 (269) T COG1652 211 TTNTVKRGDTLWQISKKVYGDGV-EYRKIAEANKALVLDNPDKIKPGQVLRIPD 263 (269) T ss_pred EEEEEECCCCHHHHHHHHCCCCC-EEEHHHHHHCCCCCCCCCCCCCCCEEECCC T ss_conf 27897038844231286608721-110488761421157835367887764686 No 31 >TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit; InterPro: IPR010243 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry describes orthologues of the beta subunit of bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription. Probab=91.82 E-value=0.41 Score=26.67 Aligned_cols=162 Identities=21% Similarity=0.260 Sum_probs=87.9 Q ss_pred HCCCCHHHHHCCCCC---EEEEEE-EEECCCCCCCCC--------CCEEEEE--EECCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 301110121014454---068875-321157851246--------7236889--62388542013455766554443355 Q gi|254780879|r 411 LASSVNLQEHLKPTD---FLETFF-SVNHANNQASDD--------SELLYIH--ARFGETRTRFYRFLNPVDGSVEYFNE 476 (652) Q Consensus 411 ~a~dVDFqr~ir~GD---~f~Vly-e~~~~~g~~~~~--------geil~A~--~~~~g~~~~~yrf~~~~~~~~~yyd~ 476 (652) |+|=--..|.|+.|+ .-+|.| +...++...+.. +.++... ....|.. +... ....++|-|= T Consensus 658 yGFIETPYr~V~~g~v~~~~~v~YLtA~eEd~~~iAQa~~~lDe~g~i~~d~V~~R~~G~e---~~~~--~~~~VdyMDV 732 (1449) T TIGR02013 658 YGFIETPYRKVKDGKVVVDDEVDYLTADEEDNYVIAQANAPLDENGRIVEDLVVARYRGDE---ITLV--SPDEVDYMDV 732 (1449) T ss_pred CCCCCCCCEEEECCEEEECCCCEECCHHHHCCEEEECCCCCCCCCCCCCCCEEEEEECCCC---CCCC--CCCCEEEEEE T ss_conf 7751367678745323333641343512236716703544318897052356888654773---2211--6760247651 Q ss_pred CCCCHHH-------CCCCCCCCCCCCCCCCCCCC--CCCCCCCCCC--CCEE--ECCCCCCCEEECCCCEEEEEEEECCC Q ss_conf 6610000-------01123334541023567641--4340443464--2003--02679672797159679996530897 Q gi|254780879|r 477 NGKSSRP-------FLLRTPVPFGRMTSGFGMRY--HPILGYSRMH--TGVD--WAAPRGTPIVAVGDGIVEKANWAGGY 543 (652) Q Consensus 477 ~G~S~~k-------~llr~Pv~~~risS~Fg~R~--hPilg~~r~H--~GVD--~aAp~GTPI~Aag~G~V~~ag~~~Gy 543 (652) +.+..-. ||-.-=-+.+=|-| ||-| -|.|.-=+|= ||.= .|.=.|+=|+|=.+|+|.|. = T Consensus 733 SP~Q~VSVaAaLIPFLEHDDANRALMGs--NMQRQAVPLL~seaP~VGTGmE~~~A~DSG~~i~A~~~GvV~~V-----d 805 (1449) T TIGR02013 733 SPKQIVSVAAALIPFLEHDDANRALMGS--NMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRAGVVEYV-----D 805 (1449) T ss_pred CCHHHHHHHHHCCCCCCCCHHHHHHHHC--CCHHHCCCCCCCCCCCCCCHHHHHHHHCCCEEEEECCCCEEEEE-----E T ss_conf 8323556655426332354145665412--53123677787798823202789886235408997069789998-----4 Q ss_pred CCEEEEECC--------CC-----EEEEEH-------------HHHHHHHCCCCCCEEECCCEEEEECCC Q ss_conf 007999839--------97-----488200-------------214454118899788349589984166 Q gi|254780879|r 544 GKQTLIHHG--------NG-----YVSSYN-------------HQDAIAKNIKAGTAVKQGQIIGWIGTT 587 (652) Q Consensus 544 Gn~V~I~H~--------~G-----y~T~Ya-------------HlS~~a~gV~~G~~V~qGQvIG~vGsT 587 (652) ++.|.|+.. +| +.-.|- |+--| |++|++|..|||||===|| T Consensus 806 a~~I~v~~~~~~~~~~~~g~DPd~~~~~Y~L~Ky~RSNQ~TC~nQ~Pi---V~~GDrV~~GdvlADGPsT 872 (1449) T TIGR02013 806 AKRIVVRYKEKEEEETVSGDDPDAAIDIYRLLKYQRSNQDTCINQRPI---VSVGDRVEAGDVLADGPST 872 (1449) T ss_pred CCEEEEEECCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCEECCEEE---CCCCCEECCCCEEECCCCC T ss_conf 778899314776665557788322025750467631478840145355---0148681021277347666 No 32 >PRK02597 DNA-directed RNA polymerase subunit beta'; Provisional Probab=91.54 E-value=0.51 Score=26.03 Aligned_cols=31 Identities=16% Similarity=0.330 Sum_probs=16.1 Q ss_pred CCCCEEEEEHHHHHHHHCCCCCCEEECCCEE Q ss_conf 3997488200214454118899788349589 Q gi|254780879|r 551 HGNGYVSSYNHQDAIAKNIKAGTAVKQGQII 581 (652) Q Consensus 551 H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvI 581 (652) -.+|..|-|.-...-..-|+.|++|.-||-| T Consensus 1028 e~d~~~~ey~~~~g~~~~v~~g~~V~~ge~l 1058 (1295) T PRK02597 1028 EDDGTITEYPILPGQNVMVSDGQQVDAGEPL 1058 (1295) T ss_pred ECCCCCEECCCCCCCCEEECCCCEEECCCCC T ss_conf 2267420013455632242257366136524 No 33 >TIGR02005 PTS-IIBC-alpha PTS system, alpha-glucoside-specific IIBC component; InterPro: IPR010975 This entry represents the fused PTS enzyme II B and C domains. A gene from Clostridium has been partially characterised as a maltose transporter, while genes from Fusobacterium and Klebsiella , have been proposed to transport the five non-standard isomers of sucrose.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system. Probab=91.24 E-value=0.29 Score=27.78 Aligned_cols=67 Identities=9% Similarity=0.072 Sum_probs=55.9 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHCCCC-HHHHHHHHHHHHCCCCHHHCC Q ss_conf 1122334222665445677776401368841797089999974999-899999999854015610169 Q gi|254780879|r 252 IKIIEENRTITSPQVLIDKIPEFADDLIPIQHNTTIFDAMVHAGYS-NGDSAKIAKALKNEVRVDQLT 318 (652) Q Consensus 252 ~~~~~en~t~~~~~~~~~~~~~~~e~~v~VK~GDTL~~IL~r~Gvs-~~ei~~i~~al~~~~~~~~Lr 318 (652) ..|..-|+..+-.+...++.+-|......-|+||+-+.--.+.+.+ +++++.++++|.+.-|+..+. T Consensus 409 fLIlkFn~~tpGRe~~eEEvKLYsKadYKak~G~~~e~~~~~~~~~yedkA~~fL~ALGG~~NI~~v~ 476 (533) T TIGR02005 409 FLILKFNIATPGREDEEEEVKLYSKADYKAKKGESKESKEAELESEYEDKAAAFLQALGGKENIKDVT 476 (533) T ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCC T ss_conf 99877078975688754432212103455127875210150015786899999996368874302344 No 34 >TIGR01995 PTS-II-ABC-beta PTS system, beta-glucoside-specific IIABC component; InterPro: IPR011297 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) , is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC . These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose , , , . This entry represents a family of PTS enzyme II proteins in which all three domains are found in the same polypeptide chain and which appear to have a broad specificity for beta-glucosides including salicin (beta-D-glucose-1-salicylate) and arbutin (hydroquinone-O-beta-D-glucopyranoside) . These are distinct from the closely related sucrose-specific and trehalose-specific PTS transporters.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system. Probab=91.00 E-value=0.46 Score=26.33 Aligned_cols=68 Identities=28% Similarity=0.315 Sum_probs=52.7 Q ss_pred CCEEECCCCCCCEEECCCCEEEEE-------EEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEE Q ss_conf 200302679672797159679996-------53089700799983997488200214454118899788349589984 Q gi|254780879|r 514 TGVDWAAPRGTPIVAVGDGIVEKA-------NWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWI 584 (652) Q Consensus 514 ~GVD~aAp~GTPI~Aag~G~V~~a-------g~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~v 584 (652) +||=+ -|..+-|+|.-||+|+-. |=.+-.|==|.| |= |.-|.=..=.-|--.|++|++|++||..+.+ T Consensus 538 ~G~Ai-~P~eG~~~AP~dG~v~~VF~T~HAiGi~~~nG~E~LI-Hv-GIDTV~L~G~~Fe~~V~~Gd~v~~Gq~L~~~ 612 (660) T TIGR01995 538 KGVAI-LPSEGEVVAPVDGTVTAVFPTKHAIGIRSDNGVEILI-HV-GIDTVELKGEYFEILVKVGDKVKAGQLLLTF 612 (660) T ss_pred CCEEE-EECCCEEECCCCCEEEEEECCCCEEEECCCCCEEEEE-EE-EEEEEEECCEEEEEEEEECCEEEECCCCCEE T ss_conf 84589-7158778823377899997486227412689728999-84-1234565450122214566787506631221 No 35 >PRK10255 N-acetyl glucosamine specific PTS system components IIABC; Provisional Probab=90.54 E-value=1.2 Score=23.35 Aligned_cols=85 Identities=18% Similarity=0.200 Sum_probs=56.3 Q ss_pred CCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEE-------CCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEE Q ss_conf 4340443464200302679672797159679996530-------897007999839974882002144541188997883 Q gi|254780879|r 504 HPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWA-------GGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVK 576 (652) Q Consensus 504 hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~-------~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~ 576 (652) +|++-..-|-+|+-+- |..--|+|.-||+|+..=.. .--|--|.| |= |..|+=..=..|-.-|++||+|+ T Consensus 517 D~vFa~~~mG~G~aI~-P~~g~v~aP~dG~i~~vf~T~HA~gi~~~~G~EiLi-Hi-GiDTV~L~G~gF~~~v~~Gd~Vk 593 (648) T PRK10255 517 DEAFASKAVGDGVAVK-PTDKIVVSPAAGTIVKIFNTNHAFCLETEKGAEIVV-HM-GIDTVALEGKGFKRLVEEGAQVS 593 (648) T ss_pred CHHHHHCCCCCCEEEE-CCCCEEECCCCCEEEEECCCCCEEEEECCCCCEEEE-EE-EECCEEECCCCCEEEECCCCEEC T ss_conf 7555314557856994-589959806885799971688579998489818999-95-44524217805348834859967 Q ss_pred CCCEEEEEC-----CCCCCC Q ss_conf 495899841-----667888 Q gi|254780879|r 577 QGQIIGWIG-----TTGLST 591 (652) Q Consensus 577 qGQvIG~vG-----sTG~ST 591 (652) +||.+..+- .-|+++ T Consensus 594 ~G~~l~~~D~~~i~~~g~~~ 613 (648) T PRK10255 594 AGQPILEMDLDYLNANARSM 613 (648) T ss_pred CCCEEEEECHHHHHHCCCCC T ss_conf 99988997499998509998 No 36 >COG2190 NagE Phosphotransferase system IIA components [Carbohydrate transport and metabolism] Probab=90.43 E-value=1.2 Score=23.51 Aligned_cols=78 Identities=24% Similarity=0.275 Sum_probs=53.4 Q ss_pred CCCCCCCCCCCEEECCCCCCCEEECCCCEEEEE-------EEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEEC Q ss_conf 340443464200302679672797159679996-------5308970079998399748820021445411889978834 Q gi|254780879|r 505 PILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKA-------NWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQ 577 (652) Q Consensus 505 Pilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~a-------g~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~q 577 (652) |++-...|-.|+-+- |..--|+|..||+|... |-..--|--+.| |= |.-|.=..=..|-.-|++|++|++ T Consensus 25 ~vFs~k~mGdGiAI~-P~~g~vvAPvdG~v~~iFpTkHAigi~t~~GvEiLi-Hi-GiDTV~L~GegF~~~v~~Gd~Vk~ 101 (156) T COG2190 25 PVFSEKMVGDGVAIK-PSEGEVVAPVDGTVVLIFPTKHAIGIETDEGVEILI-HI-GIDTVKLNGEGFESLVKEGDKVKA 101 (156) T ss_pred HHHHCCCCCCCEEEE-CCCCEEEECCCCEEEEEEECCCEEEEECCCCCEEEE-EE-CEEEEEECCCCEEEEEECCCEECC T ss_conf 676415634867994-689959812685899985178479998389959999-95-640586889324787507998815 Q ss_pred CCEEEEEC Q ss_conf 95899841 Q gi|254780879|r 578 GQIIGWIG 585 (652) Q Consensus 578 GQvIG~vG 585 (652) ||.+..+- T Consensus 102 Gd~Li~fD 109 (156) T COG2190 102 GDPLLEFD 109 (156) T ss_pred CCEEEEEC T ss_conf 98989997 No 37 >PRK05305 phosphatidylserine decarboxylase; Provisional Probab=89.53 E-value=1.4 Score=22.86 Aligned_cols=19 Identities=21% Similarity=0.475 Sum_probs=15.8 Q ss_pred HCCCCCCEEECCCEEEEEC Q ss_conf 1188997883495899841 Q gi|254780879|r 567 KNIKAGTAVKQGQIIGWIG 585 (652) Q Consensus 567 ~gV~~G~~V~qGQvIG~vG 585 (652) -.+++|++|+|||-||... T Consensus 160 ~~~~~g~~l~~G~r~G~I~ 178 (214) T PRK05305 160 CYVEEGDELERGERFGLIR 178 (214) T ss_pred ECCCCCCEEECCCEEEEEE T ss_conf 2267897885377773796 No 38 >CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed Probab=89.21 E-value=1.6 Score=22.50 Aligned_cols=44 Identities=11% Similarity=0.155 Sum_probs=24.3 Q ss_pred CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEE Q ss_conf 96799965308970079998399748820021445411889978834958998 Q gi|254780879|r 531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGW 583 (652) Q Consensus 531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~ 583 (652) +|.|+.. ..+.++||.+.-|.-. .=+-+. +.-|+-|++|+.++. T Consensus 1080 SGQIi~I-----~~~~ivIR~akPYLaS--~GA~vh--~~~GdlI~eGDtLvT 1123 (1350) T CHL00117 1080 SGQILII-----QVDSIVIRSAKPYLAT--PGATVH--GHYGEILYEGDTLVT 1123 (1350) T ss_pred CCCEEEE-----ECCEEEEEECCCEECC--CCCEEE--CCCCCEECCCCEEEE T ss_conf 7228998-----4787999943631259--997897--048988679987899 No 39 >COG4784 Putative Zn-dependent protease [General function prediction only] Probab=88.86 E-value=1.2 Score=23.46 Aligned_cols=21 Identities=38% Similarity=0.661 Sum_probs=13.7 Q ss_pred CCCEEECCCCCCCE-------EECCCCE Q ss_conf 42003026796727-------9715967 Q gi|254780879|r 513 HTGVDWAAPRGTPI-------VAVGDGI 533 (652) Q Consensus 513 H~GVD~aAp~GTPI-------~Aag~G~ 533 (652) ..||-|..|.|--| +|.+.|. T Consensus 294 ~Lg~tf~~P~Gf~IdN~~~Avlatg~ge 321 (479) T COG4784 294 ELGVTFDVPDGFKIDNSAEAVLATGPGE 321 (479) T ss_pred CCCEEEECCCCEEECCCHHHHHCCCCCC T ss_conf 6653885688637637468762458863 No 40 >pfam01333 Apocytochr_F_C Apocytochrome F, C-terminal. This is a sub-family of cytochrome C. See pfam00034. Probab=87.86 E-value=1.3 Score=23.03 Aligned_cols=83 Identities=16% Similarity=0.114 Sum_probs=52.5 Q ss_pred CCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCCCCEEEEEEEECC Q ss_conf 72797159679996530897007999839974882002144541188997883495899841667888742688997867 Q gi|254780879|r 524 TPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVNG 603 (652) Q Consensus 524 TPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vnG 603 (652) +..-|...|+|........-|..|.|...+|-.+.-.--..----|++|+.|+.||-+-.==+-|--- ...-||. T Consensus 3 nv~~as~~G~I~~I~~~ekg~~~vtI~t~dG~~v~~~IP~GpeliV~~G~~V~~dqpLT~nPNVGGFG--Q~etEIV--- 77 (118) T pfam01333 3 NVYNASAAGTITKITRNEKGGYEVTIETADGETVVETIPAGPELIVSEGQTVKADQPLTNNPNVGGFG--QAETEIV--- 77 (118) T ss_pred CEEECCCCEEEEEEEECCCCCEEEEEECCCCCEEEEECCCCCEEEECCCCEEECCCCCCCCCCCCCCC--CCCEEEE--- T ss_conf 54716677089997756788579999869998998853999748973898886698444599856657--6505999--- Q ss_pred EECCCCEEC Q ss_conf 883662000 Q gi|254780879|r 604 IKVDSTKVR 612 (652) Q Consensus 604 ~~VdP~~~~ 612 (652) -.||.|++ T Consensus 78 -LQ~P~Rv~ 85 (118) T pfam01333 78 -LQNPNRVQ 85 (118) T ss_pred -ECCHHHHH T ss_conf -51825845 No 41 >TIGR03309 matur_yqeB selenium-dependent molybdenum hydroxylase system protein, YqeB family. Members of this protein family are probable accessory proteins for the biosynthesis of enzymes with labile selenium-containing centers, different from selenocysteine-containing proteins. Probab=87.41 E-value=0.8 Score=24.61 Aligned_cols=19 Identities=32% Similarity=0.594 Sum_probs=13.7 Q ss_pred CCCCCEEECCCEEEEECCC Q ss_conf 8899788349589984166 Q gi|254780879|r 569 IKAGTAVKQGQIIGWIGTT 587 (652) Q Consensus 569 V~~G~~V~qGQvIG~vGsT 587 (652) .+-|+.|++||+||++|.+ T Consensus 179 ~~IGd~V~kG~vig~v~~~ 197 (256) T TIGR03309 179 KAIGDSVKKGDVIATVGDV 197 (256) T ss_pred HHCCCEEECCCEEEEECCE T ss_conf 4418968679689998998 No 42 >TIGR02971 heterocyst_DevB ABC exporter membrane fusion protein, DevB family; InterPro: IPR014315 Members of this protein are found mostly in the Cyanobacteria, but also in the Planctomycetes. DevB from Anabaena sp. (strain PCC 7120) is partially characterised as a membrane fusion protein of the DevBCA ABC exporter, probably a glycolipid exporter required for heterocyst formation. Most Cyanobacteria have one member only, but Nostoc sp. which has seven members.. Probab=87.10 E-value=0.55 Score=25.78 Aligned_cols=18 Identities=17% Similarity=0.158 Sum_probs=9.4 Q ss_pred HCCCCHHH----CCCCCEEEEE Q ss_conf 40156101----6998889999 Q gi|254780879|r 309 KNEVRVDQ----LTKDEILRIG 326 (652) Q Consensus 309 ~~~~~~~~----Lr~Gq~L~I~ 326 (652) -++.=++. ...|+.|+|. T Consensus 225 le~t~~~aRLvaP~~G~vLKi~ 246 (363) T TIGR02971 225 LELTYVKARLVAPIDGRVLKIH 246 (363) T ss_pred HHHHHHHHHHCCCCCCEEEEEC T ss_conf 8767677763078987688755 No 43 >CHL00006 consensus Probab=86.57 E-value=1.3 Score=23.09 Aligned_cols=57 Identities=19% Similarity=0.209 Sum_probs=27.4 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 3356657788998534765445788541131899989899999999999999987626884100 Q gi|254780879|r 9 KRDILFSFGDTPPILGNNDAKIFLDNRRKVSLRWLSTTFFAGITSGVIIGGSLLTALDGHQKIA 72 (652) Q Consensus 9 ~~~~~~~~g~eppl~~~~~~~~~~~~rr~vs~rw~~~t~ltg~~~~~l~g~a~~~aldg~~~~a 72 (652) ..+-+++||+-=-+.+.-+ ..-| --|..+| ||-||-.=+.=+.--+.|..+|--.|- T Consensus 307 ~~~~~v~~geavgiiaaqs--igep-gtqlt~r----tfhtggvf~~~~~~~~~~~~~g~i~f~ 363 (1372) T CHL00006 307 THGDLVELGEAVGIIAGQS--IGEP-GTQLTLR----TFHTGGVFTGGTAEHVRAPSNGKIKFN 363 (1372) T ss_pred CCCCCCCCCCEEEEEEEEC--CCCC-CCCCEEE----EEECCCCCCCCCHHHCCCCCCCEEECC T ss_conf 2687355575334774201--5887-6431244----210165213420110127767447526 No 44 >PRK05258 DNA-directed RNA polymerase subunit beta'; Provisional Probab=85.22 E-value=2.6 Score=20.98 Aligned_cols=72 Identities=18% Similarity=0.315 Sum_probs=47.7 Q ss_pred CCCCCCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEE--HHHHHHHHCCCCCCEEECCCEE Q ss_conf 4434642003026796727971596799965308970079998399748820--0214454118899788349589 Q gi|254780879|r 508 GYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSY--NHQDAIAKNIKAGTAVKQGQII 581 (652) Q Consensus 508 g~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~Y--aHlS~~a~gV~~G~~V~qGQvI 581 (652) |.-|.-.=++-.-|.|++|.+.-+|+|.+.....+....+++.....-.-.| .+..++. |+.|+.|.+||.+ T Consensus 952 GvPRl~EifeAr~pk~~aiisei~g~v~~i~~~~~~~~~~i~~~~~~~~~~y~ip~~~~l~--v~~gd~V~~G~~l 1025 (1204) T PRK05258 952 GLPRVQELFEARNPKGQAVITEVDGTVVAIEEDKADRTKEVTVKGETETRSYTIPYTARLK--VEEGDEVERGDEL 1025 (1204) T ss_pred CCCCHHHHHHCCCCCCCCEEEEECCEEEEEEECCCCEEEEEEECCCCEEEEEECCCCCEEE--EECCCEEECCCCC T ss_conf 7602899985047788612675145688745426741799997799648999805775687--7059998448762 No 45 >TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit; InterPro: IPR012754 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry represents the beta-prime subunit, RpoC, found in most bacteria. It excludes some, mainly cyanobacterial, species where RpoC is replaced by two homologous proteins that include an additional domain. One arm of the "claw" is predominantly formed by this subunit, the other being predominantly formed by the beta subunit. The active site of the enzyme is defined by three invariant aspartate residues within the beta-prime subunit .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription. Probab=84.27 E-value=2 Score=21.83 Aligned_cols=66 Identities=20% Similarity=0.199 Sum_probs=46.4 Q ss_pred CEEECCCCC--CCEEECCCCEEEEEEEECCCCCEEEEECCC---CEEEEEHHHHHHHHCCCCCCEEECCCEE Q ss_conf 003026796--727971596799965308970079998399---7488200214454118899788349589 Q gi|254780879|r 515 GVDWAAPRG--TPIVAVGDGIVEKANWAGGYGKQTLIHHGN---GYVSSYNHQDAIAKNIKAGTAVKQGQII 581 (652) Q Consensus 515 GVD~aAp~G--TPI~Aag~G~V~~ag~~~GyGn~V~I~H~~---Gy~T~YaHlS~~a~gV~~G~~V~qGQvI 581 (652) =.|=..|.| --++|=-||+|.+.+..---.+.|.|+-++ .+.+.+=-+.+=. -|+.|++|+.||.| T Consensus 1324 LFEar~PK~~e~A~Iae~dG~v~~~~~~~k~~r~~~i~~e~~~~e~~~Y~Ip~~~~L-~V~~G~~V~~G~~l 1394 (1552) T TIGR02386 1324 LFEARTPKDFEAAVIAEVDGVVEIIEDDVKNKRVVVIKDENDDGEEKEYLIPFGAQL-RVKDGDSVSAGDKL 1394 (1552) T ss_pred HHHCCCCCCCCCCCEEHCCCEEEEECCCCCCEEEEEEECCCCCCCEEEEEEECCCEE-EEECCCEEECCCEE T ss_conf 860168861121100010217885114423408999831688853478765066658-97218887078520 No 46 >PRK09603 DNA-directed RNA polymerase subunit beta/beta'; Reviewed Probab=84.24 E-value=2.9 Score=20.67 Aligned_cols=108 Identities=21% Similarity=0.316 Sum_probs=61.1 Q ss_pred CCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHH-HHHHHCCCCCCEEECCCEEEEECCCCCCCCCE----- Q ss_conf 796727971596799965308970079998399748820021-44541188997883495899841667888742----- Q gi|254780879|r 521 PRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQ-DAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPH----- 594 (652) Q Consensus 521 p~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHl-S~~a~gV~~G~~V~qGQvIG~vGsTG~STGPH----- 594 (652) |.-.-|.|--+|+|.+.....|--.. +|...+|-.+.|.=- ++. --|..|+.|+.||.+- .|. --|| T Consensus 2661 PK~~ailae~~G~V~~g~~~~~~~~i-ii~~~dg~~~ey~i~~g~~-l~V~~Gd~V~~Ge~Lt----dG~-inphdIL~i 2733 (2890) T PRK09603 2661 PKDVAILSEVDGIVSFGKPIRNKEHI-IVTSKDGRSMDYFVDKGKQ-ILVHADEFVHAGEAMT----DGV-VSSHDILRI 2733 (2890) T ss_pred CCCCEEEECCCCEEEECCCCCCCEEE-EEECCCCCEEEEECCCCCE-EEECCCCEEECCCCCC----CCC-CCHHHHHHH T ss_conf 88743895365189956534785269-9976999477775489987-7767998870688823----799-998999984 Q ss_pred ---------------------------EEEEEEECCEECCCCEECCCC-CCCCCHHH--HHHHHHHHHHHHH Q ss_conf ---------------------------688997867883662000788-78788899--9999999999999 Q gi|254780879|r 595 ---------------------------LHYELIVNGIKVDSTKVRIPE-RENLKGDL--LQRFAMEKKRINS 636 (652) Q Consensus 595 ---------------------------LHfEv~vnG~~VdP~~~~lp~-~~~l~~~~--l~~F~~~~~~id~ 636 (652) =|.||+|.- -..=.+|.-|. ..-|+|+. +..|+.+-+++.. T Consensus 2734 ~g~~~lq~yLVnEVQ~VYrsQGV~InDKHIEVIVRQ-MtsKV~I~d~GDT~fLpGElV~~~~~e~~N~~~~~ 2804 (2890) T PRK09603 2734 SGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQ-MLRQVRILDSGDSKFIEGDLVSKKLFKEENARVIA 2804 (2890) T ss_pred HCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEE-CCCEEEEECCCCCCCCCCCEEEHHHHHHHHHHHHH T ss_conf 079999999999999999966985536278998751-37469995688888788567629999999999997 No 47 >pfam02666 PS_Dcarbxylase Phosphatidylserine decarboxylase. This is a family of phosphatidylserine decarboxylases, EC:4.1.1.65. These enzymes catalyse the reaction: Phosphatidyl-L-serine <= phosphatidylethanolamine + CO2. Phosphatidylserine decarboxylase plays a central role in the biosynthesis of aminophospholipids by converting phosphatidylserine to phosphatidylethanolamine. Probab=83.78 E-value=3 Score=20.54 Aligned_cols=17 Identities=29% Similarity=0.626 Sum_probs=9.7 Q ss_pred CCCCEEECCCEEEEECC Q ss_conf 89978834958998416 Q gi|254780879|r 570 KAGTAVKQGQIIGWIGT 586 (652) Q Consensus 570 ~~G~~V~qGQvIG~vGs 586 (652) ++|+.|++||-||+--- T Consensus 153 ~~g~~v~kG~e~G~f~f 169 (201) T pfam02666 153 EEGDEVKKGDELGYFKF 169 (201) T ss_pred CCCCEEECCCEEEEEEC T ss_conf 58979845748807962 No 48 >PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed Probab=83.49 E-value=1.7 Score=22.37 Aligned_cols=54 Identities=28% Similarity=0.509 Sum_probs=34.0 Q ss_pred CCCCCEEECCCCEEEEEEEECCCCCEEEEECCCC------EEEEEH-------------HHHHHHHCCCCCCEEECCCEE Q ss_conf 7967279715967999653089700799983997------488200-------------214454118899788349589 Q gi|254780879|r 521 PRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNG------YVSSYN-------------HQDAIAKNIKAGTAVKQGQII 581 (652) Q Consensus 521 p~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~G------y~T~Ya-------------HlS~~a~gV~~G~~V~qGQvI 581 (652) -.|+-|.|-.+|+|.|.. ++.|.|+..+. ..-.|- |+- +-|+.|++|+.||+| T Consensus 647 ds~~~~~a~~~G~v~yvd-----~~~I~i~~~~~~~~~~~~~~~y~l~~y~~sNq~T~~~Q~---PlV~~~~~v~~~~~i 718 (1127) T PRK00405 647 DSGAVVVAKRDGVVEYVD-----ASRIVVRVNDDLAGDEGGVDIYNLTKFTRSNQNTCINQR---PIVKVGDRVEKGDVL 718 (1127) T ss_pred HHCCEEEECCCCEEEEEE-----CCEEEEEECCCCCCCCCCEEEEECCCCCCCCCCCCCCEE---EEEECCCEEECCCEE T ss_conf 417047854795599974-----788999826545677776379961313666667535640---377339888338781 Q ss_pred E Q ss_conf 9 Q gi|254780879|r 582 G 582 (652) Q Consensus 582 G 582 (652) + T Consensus 719 a 719 (1127) T PRK00405 719 A 719 (1127) T ss_pred C T ss_conf 4 No 49 >PRK06302 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated Probab=83.15 E-value=0.82 Score=24.55 Aligned_cols=21 Identities=29% Similarity=0.517 Sum_probs=13.6 Q ss_pred CCCCCEEECCCEEEEECCCCC Q ss_conf 889978834958998416678 Q gi|254780879|r 569 IKAGTAVKQGQIIGWIGTTGL 589 (652) Q Consensus 569 V~~G~~V~qGQvIG~vGsTG~ 589 (652) |++|++|+.||+|+++=.=.+ T Consensus 102 V~vGd~V~~Gq~v~iIEaMK~ 122 (155) T PRK06302 102 VEVGDTVKEGQTLCIIEAMKM 122 (155) T ss_pred CCCCCEECCCCEEEEEEECCC T ss_conf 246867248988999984243 No 50 >PRK10260 hypothetical protein; Provisional Probab=82.81 E-value=3.3 Score=20.28 Aligned_cols=47 Identities=13% Similarity=0.031 Sum_probs=38.2 Q ss_pred EEEEECCCCC--HHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEE Q ss_conf 3688417970--89999974999899999999854015610169988899997 Q gi|254780879|r 277 DLIPIQHNTT--IFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGV 327 (652) Q Consensus 277 ~~v~VK~GDT--L~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~ 327 (652) ..++++.||| |.+|+++|++...++.++ |...+.---.+|.++.|+. T Consensus 41 ~~~~v~~~dt~~L~diAr~y~lG~~ei~~A----NP~vDp~lP~~G~~l~iP~ 89 (306) T PRK10260 41 QVITIPEGNTQPLEYFAAEYQMGLSNMMEA----NPGVDTFLPKGGTVLNIPQ 89 (306) T ss_pred EEEEECCCCCHHHHHHHHHHCCCHHHHHHH----CCCCCCCCCCCCCEEEECC T ss_conf 699947897223999999858058999986----8899986699998898146 No 51 >COG0511 AccB Biotin carboxyl carrier protein [Lipid metabolism] Probab=80.23 E-value=2.4 Score=21.32 Aligned_cols=57 Identities=26% Similarity=0.278 Sum_probs=35.0 Q ss_pred CCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCC-----CCCCCCEEE Q ss_conf 967279715967999653089700799983997488200214454118899788349589984166-----788874268 Q gi|254780879|r 522 RGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTT-----GLSTGPHLH 596 (652) Q Consensus 522 ~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsT-----G~STGPHLH 596 (652) .++.|.|.--|+|.+ + -|++|++|+.||++..+=.= =-|...-.= T Consensus 69 ~~~~V~SPm~Gtv~~----------------------------~--~V~vGd~V~~Gq~l~IiEAMKmeneI~A~~~G~V 118 (140) T COG0511 69 GGTQVTSPMVGTVYK----------------------------P--FVEVGDTVKAGQTLAIIEAMKMENEIEAPADGVV 118 (140) T ss_pred CCCEEECCCCEEEEE----------------------------E--EECCCCEECCCCEEEEEEEEECCCEECCCCCCEE T ss_conf 786674787618999----------------------------8--7657999758999999982001553228999689 Q ss_pred EEEE-ECCEECCC Q ss_conf 8997-86788366 Q gi|254780879|r 597 YELI-VNGIKVDS 608 (652) Q Consensus 597 fEv~-vnG~~VdP 608 (652) =||+ .||.+|++ T Consensus 119 ~~Ilv~~G~~Ve~ 131 (140) T COG0511 119 KEILVKNGDPVEY 131 (140) T ss_pred EEEEECCCCCCCC T ss_conf 9999448985268 No 52 >PRK02693 apocytochrome f; Reviewed Probab=78.83 E-value=4.5 Score=19.38 Aligned_cols=81 Identities=17% Similarity=0.167 Sum_probs=53.6 Q ss_pred CCCEEECCCCEEEEEEEECCCCCEEEEECCCCE---EEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCCCCEEEEEE Q ss_conf 672797159679996530897007999839974---88200214454118899788349589984166788874268899 Q gi|254780879|r 523 GTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGY---VSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYEL 599 (652) Q Consensus 523 GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy---~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfEv 599 (652) -|..-|...|+|........-|..|.|...+|- +|.-+-..-+ |++|+.|+.||-+-.==+-|--- +..-|| T Consensus 196 N~~~~as~~G~I~~I~~~e~G~~~v~I~t~~G~~v~~~iP~Gp~li---V~~G~~v~~~qpLT~nPNVGGFG--Q~d~EI 270 (312) T PRK02693 196 NNVFTASAAGTITSIETGEDGSYVVTITTEDGEVVTETIPAGPELI---VKEGDAVEAGAPLTNDPNVGGFG--QLDTEI 270 (312) T ss_pred CCEECCCCCEEEEEEEECCCCCEEEEEECCCCCEEEEECCCCCEEE---ECCCCEEECCCCCCCCCCCCCCC--CCCEEE T ss_conf 7255366772788877668886799998899999988529998589---72798885698666799877667--672389 Q ss_pred EECCEECCCCEEC Q ss_conf 7867883662000 Q gi|254780879|r 600 IVNGIKVDSTKVR 612 (652) Q Consensus 600 ~vnG~~VdP~~~~ 612 (652) . -.||.||+ T Consensus 271 V----LQ~P~Ri~ 279 (312) T PRK02693 271 V----LQSPVRVK 279 (312) T ss_pred E----ECCHHHHH T ss_conf 9----22857979 No 53 >CHL00001 rpoB RNA polymerase beta subunit Probab=77.72 E-value=4.8 Score=19.16 Aligned_cols=57 Identities=23% Similarity=0.290 Sum_probs=34.5 Q ss_pred CCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEE-------------HHHHHHHHCCCCCCEEECCCEEEE Q ss_conf 26796727971596799965308970079998399748820-------------021445411889978834958998 Q gi|254780879|r 519 AAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSY-------------NHQDAIAKNIKAGTAVKQGQIIGW 583 (652) Q Consensus 519 aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~Y-------------aHlS~~a~gV~~G~~V~qGQvIG~ 583 (652) |--.|+.|.|-.+|.|.|..- +.|.|....+-.-.| .|+. +-|+.|++|+.||+|+. T Consensus 566 a~ds~~~~~a~~~G~v~y~d~-----~~i~~~~~~~~~~~y~l~~~~rsn~~t~~~q~---P~V~~g~~v~~g~ilad 635 (1065) T CHL00001 566 ALDSGVVAIAEHEGKIIYVDA-----DKIILSGNKGDTLSIPLVKYQRSNQNTCMHQK---PIVWRGECIKKGQILAD 635 (1065) T ss_pred HHCCCCEEEECCCCEEEEEEC-----CEEEEECCCCCEEEEEECCCCCCCCCCCCCCC---EEEECCCEEECCCEECC T ss_conf 320473688426862888507-----66899637885578752566668755542512---05624867712837435 No 54 >PRK09890 cold shock protein CspG; Provisional Probab=76.78 E-value=3 Score=20.62 Aligned_cols=47 Identities=21% Similarity=0.332 Sum_probs=31.7 Q ss_pred CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCC-CEEECCCEEEE Q ss_conf 967999653089700799983997488200214454118899-78834958998 Q gi|254780879|r 531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAG-TAVKQGQIIGW 583 (652) Q Consensus 531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G-~~V~qGQvIG~ 583 (652) .|+|..-.-.+|||-. ...+|=.-.|-|.|.+. ..| .....||.|-| T Consensus 6 tG~VKwFn~~KGyGFI---~~ddg~~DvFvH~s~i~---~~~~~~L~~Gq~V~f 53 (70) T PRK09890 6 TGLVKWFNADKGFGFI---TPDDGSKDVFVHFTAIQ---SNEFRTLNENQKVEF 53 (70) T ss_pred EEEEEEECCCCCEEEE---CCCCCCCCEEEEHHHHC---CCCCCCCCCCCEEEE T ss_conf 6999988399986997---03899942999868927---268833299999999 No 55 >cd06254 M14_ASTE_ASPA_like_4 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. Probab=76.08 E-value=2.1 Score=21.70 Aligned_cols=19 Identities=32% Similarity=0.770 Sum_probs=16.9 Q ss_pred CCCCCCEEECCCEEEEECC Q ss_conf 1889978834958998416 Q gi|254780879|r 568 NIKAGTAVKQGQIIGWIGT 586 (652) Q Consensus 568 gV~~G~~V~qGQvIG~vGs 586 (652) .++.|++|++||+||++=+ T Consensus 237 ~v~~G~~V~~Gq~lg~I~d 255 (288) T cd06254 237 FVKAGDTVQKGALLGYVTD 255 (288) T ss_pred ECCCCCEECCCCEEEEEEC T ss_conf 3688999768999999968 No 56 >PRK10190 hypothetical protein; Provisional Probab=75.33 E-value=5.5 Score=18.72 Aligned_cols=47 Identities=11% Similarity=0.005 Sum_probs=37.3 Q ss_pred EEEEECCCCC--HHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEE Q ss_conf 3688417970--89999974999899999999854015610169988899997 Q gi|254780879|r 277 DLIPIQHNTT--IFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGV 327 (652) Q Consensus 277 ~~v~VK~GDT--L~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~ 327 (652) ..++|.++|| |.+|+++|++...++.++ |.-.+.---++|.++.|+. T Consensus 38 ~~~~v~~~~~~~L~~iAr~y~~G~~~i~~A----NPgvDp~lP~~G~~l~iP~ 86 (310) T PRK10190 38 LTVTVPDHNTQPLETFAAQYGQGLSNMLEA----NPGADVFLPKSGSQLTIPQ 86 (310) T ss_pred EEEEECCCCCCCHHHHHHHHCHHHHHHHHH----CCCCCCCCCCCCCEEEECC T ss_conf 799937898732999999867669999986----8899987799998898066 No 57 >smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor. Probab=75.12 E-value=3.2 Score=20.39 Aligned_cols=39 Identities=23% Similarity=0.416 Sum_probs=23.4 Q ss_pred CEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHH---CCCCCCEE Q ss_conf 679996530897007999839974882002144541---18899788 Q gi|254780879|r 532 GIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAK---NIKAGTAV 575 (652) Q Consensus 532 G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~---gV~~G~~V 575 (652) |+|..- +.|||-..- .+|=...|-|+|.|.. .++.||+| T Consensus 2 G~Vk~f--~kGfGFI~~---~~g~~DvFvH~s~i~~~~~~l~~Gd~V 43 (64) T smart00357 2 GVVKWF--NKGFGFIRP---DDGGKDVFVHPSQIQGGLKSLREGDEV 43 (64) T ss_pred CEEEEE--ECCEEEEEE---CCCCCCEEEEHHHHCCCCCCCCCCCEE T ss_conf 479698--284488861---899940999869954677744758789 No 58 >pfam00313 CSD 'Cold-shock' DNA-binding domain. Probab=74.77 E-value=4.5 Score=19.38 Aligned_cols=49 Identities=24% Similarity=0.319 Sum_probs=32.6 Q ss_pred CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEE Q ss_conf 967999653089700799983997488200214454118899788349589984 Q gi|254780879|r 531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWI 584 (652) Q Consensus 531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~v 584 (652) .|+|..-.-..|||- |.-.+|-.-.|.|.|.+.. .....+++||.+-|- T Consensus 2 tG~VK~f~~~kGfGF---I~~~~~~~DiFvH~s~l~~--~~~~~L~~G~~V~f~ 50 (66) T pfam00313 2 TGTVKWFNAKKGFGF---ITPEDGDKDVFVHFSAIQG--DGFRSLQEGQRVEFD 50 (66) T ss_pred CEEEEEEECCCCEEE---EEECCCCCEEEEEHHHHCC--CCCCCCCCCCEEEEE T ss_conf 489999959999699---9978998469999268121--478617999999999 No 59 >TIGR02644 Y_phosphoryl pyrimidine-nucleoside phosphorylase; InterPro: IPR000053 Two highly similar activities are represented in this group: thymidine phosphorylase (TP, gene deoA, 2.4.2.4 from EC) and pyrimidine-nucleoside phosphorylase (PyNP, gene pdp, 2.4.2.2 from EC). Both are dimeric enzymes that function in the salvage pathway to catalyse the reversible phosphorolysis of pyrimidine nucleosides to the free base and sugar moieties. In the case of thymidine phosphorylase, thymidine (and to a lesser extent, 2'-deoxyuridine) is lysed to produce thymine (or uracil) and 2'-deoxyribose-1-phosphate. Pyrimidine-nucleoside phosphorylase performs the analogous reaction on thymidine (to produce the same products) and uridine (to produce uracil and ribose-1-phosphate). PyNP is typically the only pyrimidine nucleoside phosphorylase encoded by Gram positive bacteria, while eukaryotes and proteobacteria encode two: TP, and the unrelated uridine phosphorylase. In humans, TP was originally characterised as platelet-derived endothelial cell growth factor and gliostatin . Structurally, the enzymes are homodimers, each composed of a rigid all alpha-helix lobe and a mixed alpha-helix/beta-sheet lobe, which are connected by a flexible hinge , . Prior to substrate binding, the lobes are separated by a large cleft. A functional active site and subsequent catalysis occurs upon closing of the cleft. The active site, composed of a phosphate binding site and a (deoxy)ribonucleotide binding site within the cleft region, is highly conserved between the two enzymes of this group. Active site residues (Escherichia coli DeoA numbering) include the phosphate binding Lys84 and Ser86 (close to a glycine-rich loop), Ser113, and Thr123, and the pyrimidine nucleoside-binding Arg171, Ser186, and Lys190. Sequence comparison between the active site residues for both enzymes reveals only one difference , which has been proposed to partially mediate substrate specificity. In TP, position 111 is a methionine, while the analogous position in PyNP is lysine. It should be noted that the uncharacterised archaeal members of this family differ in a number of respects from either of the characterised activities. The residue at position 108 is lysine, indicating the activity might be PyNP-like (though the determinants of substrate specificity have not been fully elucidated). Position 171 is glutamate (negative charge side chain) rather than arginine (positive charge side chain). In addition, a large loop that may "lock in" the substrates within the active site is much smaller than in the characterised members. It is not clear what effect these and other differences have on activity and specificity.; GO: 0006206 pyrimidine base metabolic process. Probab=74.70 E-value=4.6 Score=19.29 Aligned_cols=57 Identities=25% Similarity=0.281 Sum_probs=45.7 Q ss_pred CCCCCCEEECCCCEEEEE--------EEECCCCCEE---EEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECC Q ss_conf 679672797159679996--------5308970079---998399748820021445411889978834958998416 Q gi|254780879|r 520 APRGTPIVAVGDGIVEKA--------NWAGGYGKQT---LIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGT 586 (652) Q Consensus 520 Ap~GTPI~Aag~G~V~~a--------g~~~GyGn~V---~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGs 586 (652) ++.=.+|+|--||.|.+. +|.=|-|+.- .|+|.-|..- ..+.|++|+.||+|.++=+ T Consensus 338 ~k~~~~v~A~~~G~i~~~~a~~~G~a~~~LGAGR~~k~D~ID~~aGi~l----------~~k~Gd~V~~Gd~~~tlY~ 405 (425) T TIGR02644 338 AKYKEEVKAEKSGYISEIDAEELGLAAVDLGAGRARKEDKIDHEAGIYL----------HKKVGDKVKKGDPIATLYS 405 (425) T ss_pred CCCEEEEECCCCCEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEE----------ECCCCCEEECCCEEEEEEC T ss_conf 8620233015661365107889989998615887698963001135567----------6566875323757999862 No 60 >COG3835 CdaR Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms] Probab=74.60 E-value=2.5 Score=21.11 Aligned_cols=14 Identities=7% Similarity=-0.097 Sum_probs=6.0 Q ss_pred HHHHHHHHCCCCHH Q ss_conf 25666887199989 Q gi|254780879|r 389 GIWRATSFNGMNSN 402 (652) Q Consensus 389 SLy~aa~~~gip~~ 402 (652) +++.+|....+-.+ T Consensus 327 ~l~~tA~~L~IHrN 340 (376) T COG3835 327 QLNATAEALFIHRN 340 (376) T ss_pred CHHHHHHHHCCCHH T ss_conf 99899998451051 No 61 >PRK07051 hypothetical protein; Validated Probab=73.27 E-value=2.6 Score=21.00 Aligned_cols=18 Identities=22% Similarity=0.673 Sum_probs=12.3 Q ss_pred CCCCCEEECCCEEEEECC Q ss_conf 889978834958998416 Q gi|254780879|r 569 IKAGTAVKQGQIIGWIGT 586 (652) Q Consensus 569 V~~G~~V~qGQvIG~vGs 586 (652) |++|++|+.||+|+.+=+ T Consensus 26 V~~Gd~V~~G~~v~iiEa 43 (80) T PRK07051 26 VEVGDTVAAGDVVGLVEV 43 (80) T ss_pred CCCCCEECCCCEEEEEEE T ss_conf 367999889999999970 No 62 >PRK10354 major cold shock protein; Provisional Probab=73.12 E-value=5.2 Score=18.93 Aligned_cols=33 Identities=33% Similarity=0.410 Sum_probs=25.3 Q ss_pred CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHH Q ss_conf 967999653089700799983997488200214454 Q gi|254780879|r 531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIA 566 (652) Q Consensus 531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a 566 (652) .|+|.+-.-.+|||-.. -.+|=.-.|-|.|.+. T Consensus 6 tG~VKwFn~~KGyGFI~---~d~g~~DvFvH~s~l~ 38 (70) T PRK10354 6 TGIVKWFNADKGFGFIT---PDDGSKDVFVHFSAIQ 38 (70) T ss_pred EEEEEEEECCCCEEEEE---CCCCCCEEEEEHHHHC T ss_conf 79999870999859984---2799842999858917 No 63 >cd06250 M14_PaAOTO_like An uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the the M14 family of metallocarboxypeptidases. This subgroup includes Pseudomonas aeruginosa AotO and related proteins. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. The gene encoding Probab=72.65 E-value=3.2 Score=20.42 Aligned_cols=33 Identities=15% Similarity=0.173 Sum_probs=22.1 Q ss_pred EEEEEHHHHHHH-HCCCCCCEEECCCEEEEECCC Q ss_conf 488200214454-118899788349589984166 Q gi|254780879|r 555 YVSSYNHQDAIA-KNIKAGTAVKQGQIIGWIGTT 587 (652) Q Consensus 555 y~T~YaHlS~~a-~gV~~G~~V~qGQvIG~vGsT 587 (652) +...|+-.+.+. ..++.|++|++||+||.+=+- T Consensus 289 ~~~v~Ap~~Gi~~~~~~~G~~V~~G~~la~I~dP 322 (359) T cd06250 289 VEMLYAPAGGMVVYRAAPGDWVEAGDVLAEILDP 322 (359) T ss_pred CEEEECCCCEEEEECCCCCCEECCCCEEEEEECC T ss_conf 6799569986898727999997799989999489 No 64 >cd06255 M14_ASTE_ASPA_like_5 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. Probab=72.30 E-value=2.9 Score=20.64 Aligned_cols=20 Identities=25% Similarity=0.473 Sum_probs=17.6 Q ss_pred CCCCCCEEECCCEEEEECCC Q ss_conf 18899788349589984166 Q gi|254780879|r 568 NIKAGTAVKQGQIIGWIGTT 587 (652) Q Consensus 568 gV~~G~~V~qGQvIG~vGsT 587 (652) .++.|++|++||+||++-+- T Consensus 245 ~v~~G~~V~kGq~lg~I~dp 264 (293) T cd06255 245 SVPAGDTIPAGQPLGRVVDL 264 (293) T ss_pred ECCCCCEECCCCEEEEEECC T ss_conf 37889997799999999899 No 65 >LOAD_cold consensus Probab=71.58 E-value=6.2 Score=18.38 Aligned_cols=48 Identities=27% Similarity=0.369 Sum_probs=30.3 Q ss_pred CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCC-EEECCCEEEEE Q ss_conf 9679996530897007999839974882002144541188997-88349589984 Q gi|254780879|r 531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGT-AVKQGQIIGWI 584 (652) Q Consensus 531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~-~V~qGQvIG~v 584 (652) .|+|..=.-..|||-. .-.+|-.-.|-|.|.+.. .|. .++.||.|-|- T Consensus 3 ~G~VK~f~~~kGfGFI---~~~~g~~DvFvH~s~l~~---~~~~~l~~G~~V~f~ 51 (67) T LOAD_cold 3 KGTVKWFNVKKGFGFI---TPEDGGEDVFVHQSAIQG---DGFRSLTEGQEVEFD 51 (67) T ss_pred CEEEEEEECCCCCEEE---EECCCCCEEEEEHHHHCC---CCCCCCCCCCEEEEE T ss_conf 8699999899994788---757998218999478140---478647999999999 No 66 >cd06252 M14_ASTE_ASPA_like_2 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. Probab=71.20 E-value=6.9 Score=18.06 Aligned_cols=21 Identities=29% Similarity=0.408 Sum_probs=17.8 Q ss_pred CCCCCCEEECCCEEEEECCCC Q ss_conf 188997883495899841667 Q gi|254780879|r 568 NIKAGTAVKQGQIIGWIGTTG 588 (652) Q Consensus 568 gV~~G~~V~qGQvIG~vGsTG 588 (652) .++.|++|++||+||++=+.. T Consensus 258 ~v~lG~~V~kGq~lg~I~dp~ 278 (316) T cd06252 258 LVDLGDEVSAGQVAGRIHFPE 278 (316) T ss_pred ECCCCCEECCCCEEEEEECCC T ss_conf 178899977999999996887 No 67 >COG3858 Predicted glycosyl hydrolase [General function prediction only] Probab=70.75 E-value=6.1 Score=18.42 Aligned_cols=53 Identities=13% Similarity=0.089 Sum_probs=38.0 Q ss_pred CEEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECCCC Q ss_conf 013688417970899999749998999999998540156101699888999972788 Q gi|254780879|r 275 ADDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQKD 331 (652) Q Consensus 275 ~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~~~ 331 (652) ......|++|||+.+|+++.|++.+.+..+ +....-..|..|-.|.++..++. T Consensus 48 ~~~~y~~~~~d~~~Sia~~~~vt~~~~~~m----~~~~~~~~l~~~~~l~~P~~~~~ 100 (423) T COG3858 48 SGHFYDVGPGDTLTSIARTVGVTQDSAAIM----NFVICPGYLQYGLNLYIPSARKT 100 (423) T ss_pred CCEEEEECCCCCHHHHHHHHCCCHHHHHHH----CCCCCCCCEEEEEEEECCCCCCC T ss_conf 534998247740433342114778898763----11146610542257852577777 No 68 >TIGR01945 rnfC electron transport complex, RnfABCDGE type, C subunit; InterPro: IPR010208 The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation . A closely related complex in Escherichia coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized . This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase (IPR003667 from INTERPRO), but is distinct. This entry describes the C subunit.; GO: 0051539 4 iron 4 sulfur cluster binding, 0006118 electron transport, 0016020 membrane. Probab=70.34 E-value=2.1 Score=21.71 Aligned_cols=17 Identities=24% Similarity=0.135 Sum_probs=8.0 Q ss_pred CCCCHHHHHHHHCCCCC Q ss_conf 55650334432023332 Q gi|254780879|r 202 HTAQDEEIKNAIMNQFF 218 (652) Q Consensus 202 ~~~~~~~~~~~~~~~~~ 218 (652) ..++.+++...++.++- T Consensus 120 ~~l~~~~i~~~I~~AGI 136 (444) T TIGR01945 120 SSLSPEEILEKIRAAGI 136 (444) T ss_pred HHCCHHHHHHHHHHCCC T ss_conf 31487999999997086 No 69 >cd06251 M14_ASTE_ASPA_like_1 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. Probab=70.26 E-value=2.8 Score=20.81 Aligned_cols=18 Identities=39% Similarity=0.634 Sum_probs=16.0 Q ss_pred CCCCCEEECCCEEEEECC Q ss_conf 889978834958998416 Q gi|254780879|r 569 IKAGTAVKQGQIIGWIGT 586 (652) Q Consensus 569 V~~G~~V~qGQvIG~vGs 586 (652) ++.|++|++||+||++=+ T Consensus 234 ~~~G~~V~~Gq~lg~I~d 251 (287) T cd06251 234 VKLGDKVKKGQLLATITD 251 (287) T ss_pred CCCCCEECCCCEEEEEEC T ss_conf 898899479998999978 No 70 >cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription. Probab=70.11 E-value=6.1 Score=18.41 Aligned_cols=49 Identities=18% Similarity=0.279 Sum_probs=29.7 Q ss_pred CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEE Q ss_conf 967999653089700799983997488200214454118899788349589984 Q gi|254780879|r 531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWI 584 (652) Q Consensus 531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~v 584 (652) .|+|..-....|||-.. -.++=.-.|-|.|.|... --.+.+.||.+-|. T Consensus 2 ~G~Vk~f~~~kGfGFI~---~~~~~~diF~H~s~~~~~--~~~~l~~G~~V~f~ 50 (65) T cd04458 2 TGTVKWFDDEKGFGFIT---PDDGGEDVFVHISALEGD--GFRSLEEGDRVEFE 50 (65) T ss_pred EEEEEEEECCCCEEEEE---ECCCCCCEEEEHHHHCCC--CCCCCCCCCEEEEE T ss_conf 38999997999969999---579982299995892434--69747989899999 No 71 >cd06253 M14_ASTE_ASPA_like_3 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. Probab=69.61 E-value=3.7 Score=19.99 Aligned_cols=20 Identities=35% Similarity=0.478 Sum_probs=16.9 Q ss_pred CCCCCCEEECCCEEEEECCC Q ss_conf 18899788349589984166 Q gi|254780879|r 568 NIKAGTAVKQGQIIGWIGTT 587 (652) Q Consensus 568 gV~~G~~V~qGQvIG~vGsT 587 (652) -++.|++|++||+||++=+. T Consensus 243 ~~~lG~~V~~G~~lg~I~dp 262 (298) T cd06253 243 AKHLGDIVKRGDVIGEIVDP 262 (298) T ss_pred ECCCCCEECCCCEEEEEECC T ss_conf 46889988789999999688 No 72 >PRK10476 multidrug resistance protein MdtN; Provisional Probab=69.17 E-value=7.6 Score=17.77 Aligned_cols=14 Identities=7% Similarity=0.204 Sum_probs=9.4 Q ss_pred HHCCCCCEEEEEEE Q ss_conf 10144540688753 Q gi|254780879|r 419 EHLKPTDFLETFFS 432 (652) Q Consensus 419 r~ir~GD~f~Vlye 432 (652) .++++|+..+|.+. T Consensus 259 ~~v~~Gq~v~I~~D 272 (348) T PRK10476 259 KNIRVGDCATVYSM 272 (348) T ss_pred CCCCCCCEEEEEEE T ss_conf 52799898999997 No 73 >PRK05352 Na(+)-translocating NADH-quinone reductase subunit A; Provisional Probab=69.07 E-value=3 Score=20.58 Aligned_cols=16 Identities=13% Similarity=0.333 Sum_probs=6.6 Q ss_pred CCCHHHHHHHHCCCCC Q ss_conf 5650334432023332 Q gi|254780879|r 203 TAQDEEIKNAIMNQFF 218 (652) Q Consensus 203 ~~~~~~~~~~~~~~~~ 218 (652) .++.+++...+.+++. T Consensus 113 ~ls~e~i~~~L~~sGl 128 (448) T PRK05352 113 SLSREQVKENLLESGL 128 (448) T ss_pred HCCHHHHHHHHHHCCC T ss_conf 5699999999986698 No 74 >COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion] Probab=68.88 E-value=7.7 Score=17.73 Aligned_cols=53 Identities=15% Similarity=0.201 Sum_probs=38.5 Q ss_pred EEEEEECCCCCHHHHHHHC----CCCHHHHHHHHHHHHC----CCCHHHCCCCCEEEEEEC Q ss_conf 1368841797089999974----9998999999998540----156101699888999972 Q gi|254780879|r 276 DDLIPIQHNTTIFDAMVHA----GYSNGDSAKIAKALKN----EVRVDQLTKDEILRIGVV 328 (652) Q Consensus 276 e~~v~VK~GDTL~~IL~r~----Gvs~~ei~~i~~al~~----~~~~~~Lr~Gq~L~I~~~ 328 (652) -..+++++||||++|..+. +++..+....+-.+|. ..++++|+.|..|+|+.. T Consensus 188 g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP~~ 248 (755) T COG3170 188 GDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIPSA 248 (755) T ss_pred CCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCHHHHCCCCHHHCCCCCEEECCCH T ss_conf 7666668760499998741676643199999999860915422651421334544524602 No 75 >PRK05820 deoA thymidine phosphorylase; Reviewed Probab=68.24 E-value=7.9 Score=17.64 Aligned_cols=57 Identities=21% Similarity=0.295 Sum_probs=42.4 Q ss_pred CCCCCCEEECCCCEEEEEE--------EECCCCCEE---EEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECC Q ss_conf 6796727971596799965--------308970079---998399748820021445411889978834958998416 Q gi|254780879|r 520 APRGTPIVAVGDGIVEKAN--------WAGGYGKQT---LIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGT 586 (652) Q Consensus 520 Ap~GTPI~Aag~G~V~~ag--------~~~GyGn~V---~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGs 586 (652) ++.=.+|.|..+|.|.... +.=|-|+.. .|+|.-|++- -++.|++|++||.|..+=+ T Consensus 337 a~~~~~i~A~~~G~v~~id~~~iG~a~v~LGaGR~~~~d~ID~~vGi~l----------~~k~Gd~V~kGdpl~~iya 404 (440) T PRK05820 337 APVIKPVYADRSGFLSAMDTRALGMAVVRLGGGRRRPGDPIDYSVGLTL----------HARLGDRVDAGEPLATLHA 404 (440) T ss_pred CCEEEEEECCCCEEEEEECHHHHHHHHHHCCCCCCCCCCCCCCCCCEEE----------ECCCCCEECCCCEEEEEEC T ss_conf 8868999728966999853799999999808873678987682668588----------5158899679994999974 No 76 >PRK10943 cold shock-like protein CspC; Provisional Probab=67.49 E-value=6.9 Score=18.03 Aligned_cols=48 Identities=27% Similarity=0.370 Sum_probs=31.5 Q ss_pred CCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCC-CEEECCCEEEE Q ss_conf 5967999653089700799983997488200214454118899-78834958998 Q gi|254780879|r 530 GDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAG-TAVKQGQIIGW 583 (652) Q Consensus 530 g~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G-~~V~qGQvIG~ 583 (652) -.|+|.+-....|||-.. -.+|=.-.|-|.|.+. ..| .....||.|-| T Consensus 4 ~~G~VKwFn~~kGfGFI~---~~dg~~DvFvH~s~i~---~~g~~~L~eGq~V~f 52 (69) T PRK10943 4 IKGQVKWFNESKGFGFIT---PADGSKDVFVHFSAIQ---GNGFKTLAEGQNVEF 52 (69) T ss_pred EEEEEEEEECCCCEEEEE---ECCCCCCEEEEHHHHC---CCCCCCCCCCCEEEE T ss_conf 788999983999869986---1799830999938827---168832399999999 No 77 >PRK04192 V-type ATP synthase subunit A; Provisional Probab=66.91 E-value=7.4 Score=17.83 Aligned_cols=22 Identities=27% Similarity=0.435 Sum_probs=14.8 Q ss_pred CCEEEEECCCCCCCCCEEEEEE Q ss_conf 9589984166788874268899 Q gi|254780879|r 578 GQIIGWIGTTGLSTGPHLHYEL 599 (652) Q Consensus 578 GQvIG~vGsTG~STGPHLHfEv 599 (652) -++|-.||.-++|---+|.+|+ T Consensus 471 ~eiv~lvG~d~l~~~~~l~l~~ 492 (585) T PRK04192 471 QEIVRLVGEDALSEEDRLILEV 492 (585) T ss_pred HHHHHHHCCCCCCHHHHHHHHH T ss_conf 9999864775589889789999 No 78 >cd05830 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5 represented by Streptomyces avermitilis SAV4337. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell. Probab=66.40 E-value=4.6 Score=19.31 Aligned_cols=31 Identities=23% Similarity=0.508 Sum_probs=14.6 Q ss_pred CCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEE Q ss_conf 89700799983997488200214454118899788 Q gi|254780879|r 541 GGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAV 575 (652) Q Consensus 541 ~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V 575 (652) |..||+|+-=|.++|-..+.+|.+ +++|+.| T Consensus 42 G~~Gn~viaGHr~~~~~~F~~L~~----l~~GD~I 72 (137) T cd05830 42 GEVGNFAVAGHRTTYGAPFNDLDK----LRPGDKI 72 (137) T ss_pred CCCCEEEEEECCCCCCCCCCCHHC----CCCCCEE T ss_conf 999719999722897755601353----8999999 No 79 >pfam09070 PFU PFU (PLAA family ubiquitin binding). This domain is found N terminal to pfam08324 and binds to ubiquitin. Probab=66.28 E-value=8.6 Score=17.38 Aligned_cols=44 Identities=30% Similarity=0.526 Sum_probs=32.8 Q ss_pred CCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCCCCEEE Q ss_conf 700799983997488200214454118899788349589984166788874268 Q gi|254780879|r 543 YGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLH 596 (652) Q Consensus 543 yGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLH 596 (652) -|-..+||+++|-..+|.-- .|+|++-|+|++- ++|.+.|-.+| T Consensus 7 eGq~~~vr~~~g~veAyqWs--------~~~W~kIG~Vv~~--~~~~~~~k~~~ 50 (115) T pfam09070 7 EGQVKMVKNGDGKVEAYQWS--------EGRWVKIGDVVDG--SSGSSGGKVLY 50 (115) T ss_pred CCCEEEEECCCCCEEEEEEC--------CCCEEEEEEEECC--CCCCCCCCCCC T ss_conf 77189999899969999834--------4735898889827--88877884012 No 80 >PRK06078 pyrimidine-nucleoside phosphorylase; Reviewed Probab=66.02 E-value=7.6 Score=17.76 Aligned_cols=57 Identities=26% Similarity=0.263 Sum_probs=42.9 Q ss_pred CCCCCCEEECCCCEEEEE-----E---EECCCCCEE---EEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECC Q ss_conf 679672797159679996-----5---308970079---998399748820021445411889978834958998416 Q gi|254780879|r 520 APRGTPIVAVGDGIVEKA-----N---WAGGYGKQT---LIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGT 586 (652) Q Consensus 520 Ap~GTPI~Aag~G~V~~a-----g---~~~GyGn~V---~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGs 586 (652) ++.-.+|.|.-+|.|... | +.=|.|+.. .|+|+-|+.- -++.|++|++||.|..+=+ T Consensus 332 a~~~~~i~A~~~G~V~~id~~~iG~a~~~LGaGR~~~~D~ID~~vGi~l----------~~k~Gd~V~kGdpL~tiya 399 (434) T PRK06078 332 AKYQIEVPAKESGYISEIVADEIGLAAMLLGAGRATKEDEIDLAVGIVL----------RKKVGDSVKKGESLVTIYA 399 (434) T ss_pred CCEEEEEECCCCEEEEEECHHHHHHHHHHCCCCCCCCCCCCCCCCCEEE----------ECCCCCEECCCCEEEEEEC T ss_conf 8868999738865999954899999999839997888888885768487----------2569599579994999974 No 81 >COG3608 Predicted deacylase [General function prediction only] Probab=64.54 E-value=9.2 Score=17.15 Aligned_cols=35 Identities=26% Similarity=0.406 Sum_probs=24.4 Q ss_pred CCCCCEEECCCEEEEECCCCCCCCCEEEEEEE--ECCEEC Q ss_conf 88997883495899841667888742688997--867883 Q gi|254780879|r 569 IKAGTAVKQGQIIGWIGTTGLSTGPHLHYELI--VNGIKV 606 (652) Q Consensus 569 V~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~--vnG~~V 606 (652) |+.|++|.+||+++++=+-|+.- +-=||+ ++|..+ T Consensus 271 v~lGd~VeaG~~la~i~~~~~~~---~~~eirA~~~G~i~ 307 (331) T COG3608 271 VDLGDKVEAGDVLATIHDPPLGE---GEAEIRAPVSGIII 307 (331) T ss_pred ECCCCCCCCCCEEEEEECCCCCC---CCEEEECCCCCEEE T ss_conf 16788021787679973688887---52589727882699 No 82 >COG0187 GyrB Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit [DNA replication, recombination, and repair] Probab=64.46 E-value=6 Score=18.47 Aligned_cols=14 Identities=14% Similarity=0.420 Sum_probs=6.5 Q ss_pred HHHHHHHHHCCCCC Q ss_conf 99999998414776 Q gi|254780879|r 631 KKRINSLLNNGENP 644 (652) Q Consensus 631 ~~~id~ll~~~~~~ 644 (652) .+.++.||.....| T Consensus 605 d~~f~~LMGd~ve~ 618 (635) T COG0187 605 DEIFSTLMGDKVEP 618 (635) T ss_pred HHHHHHHCCCCCHH T ss_conf 99999870778568 No 83 >CHL00037 petA cytochrome f Probab=64.30 E-value=9.3 Score=17.12 Aligned_cols=81 Identities=20% Similarity=0.131 Sum_probs=48.3 Q ss_pred CCCEEECCCCEEEEEEEECCCCCEEEE-ECCCCEEE---EEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCCCCEEEEE Q ss_conf 672797159679996530897007999-83997488---20021445411889978834958998416678887426889 Q gi|254780879|r 523 GTPIVAVGDGIVEKANWAGGYGKQTLI-HHGNGYVS---SYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYE 598 (652) Q Consensus 523 GTPI~Aag~G~V~~ag~~~GyGn~V~I-~H~~Gy~T---~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfE 598 (652) -|..-|...|+|.......--|..|.| +..+|-.+ .=.-..- -|++|+.|+.||-+-.==+-|--- +..-| T Consensus 203 N~~~~as~~G~i~~I~~~ekgg~~itI~~~~dG~~v~~~iP~Gpel---~V~eG~~vk~dqpLT~nPNVGGFG--Q~e~E 277 (320) T CHL00037 203 NTVYNATAAGIVSKIIRKEKGGYEITIVDASDGRQVVDIIPPGPEL---LVSEGESIKLDQPLTSNPNVGGFG--QGDAE 277 (320) T ss_pred CCEECCCCCCEEEEEEECCCCCEEEEEEECCCCCEEEEECCCCCEE---EECCCCEEECCCCCCCCCCCCCCC--CCCEE T ss_conf 8266055772788877657895699998658997888744999758---972798885698555699867667--66148 Q ss_pred EEECCEECCCCEEC Q ss_conf 97867883662000 Q gi|254780879|r 599 LIVNGIKVDSTKVR 612 (652) Q Consensus 599 v~vnG~~VdP~~~~ 612 (652) |. -.||.|++ T Consensus 278 IV----LQ~P~Rv~ 287 (320) T CHL00037 278 IV----LQDPLRVQ 287 (320) T ss_pred EE----ECCHHHHH T ss_conf 99----41835846 No 84 >PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional Probab=64.18 E-value=8.8 Score=17.29 Aligned_cols=48 Identities=27% Similarity=0.354 Sum_probs=31.7 Q ss_pred CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCC-CEEECCCEEEEE Q ss_conf 967999653089700799983997488200214454118899-788349589984 Q gi|254780879|r 531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAG-TAVKQGQIIGWI 584 (652) Q Consensus 531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G-~~V~qGQvIG~v 584 (652) .|+|..-.-.+|||-.. -.+|=.-.|.|.|.|. ..| ...+.||.|-|. T Consensus 3 ~G~VKwFn~~KGyGFI~---~d~gg~DvFvH~s~i~---~~G~~~L~~G~~V~f~ 51 (74) T PRK09937 3 KGTVKWFNNAKGFGFIC---PEGGGEDIFAHYSTIQ---MDGYRTLKAGQSVQFD 51 (74) T ss_pred CCEEEEEECCCCEEEEE---ECCCCCCEEEEHHHHC---CCCCCCCCCCCEEEEE T ss_conf 83797883899718862---0799955999858823---1588424999999999 No 85 >COG1278 CspC Cold shock proteins [Transcription] Probab=64.13 E-value=6.4 Score=18.27 Aligned_cols=43 Identities=28% Similarity=0.444 Sum_probs=31.0 Q ss_pred CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHH----HCCCCCCEEE Q ss_conf 967999653089700799983997488200214454----1188997883 Q gi|254780879|r 531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIA----KNIKAGTAVK 576 (652) Q Consensus 531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a----~gV~~G~~V~ 576 (652) .|+|..-...+|||- |.-.+|=.-.|.|.|.|- +.+.+||+|. T Consensus 3 ~GtVKwfn~~KGfGF---I~p~~G~~DvFVH~Sai~~~g~~~L~eGQ~V~ 49 (67) T COG1278 3 TGTVKWFNATKGFGF---ITPEDGGKDVFVHISAIQRAGFRTLREGQKVE 49 (67) T ss_pred CCEEEEEECCCCCEE---ECCCCCCCCEEEEEEEECCCCCCCCCCCCEEE T ss_conf 616888508986337---07899985779980125127886557998899 No 86 >pfam00529 HlyD HlyD family secretion protein. Probab=64.09 E-value=5.1 Score=18.97 Aligned_cols=26 Identities=19% Similarity=0.244 Sum_probs=13.8 Q ss_pred CCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEE Q ss_conf 007999839974882002144541188997883 Q gi|254780879|r 544 GKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVK 576 (652) Q Consensus 544 Gn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~ 576 (652) +.-|+|.=.+ .|. .+..|+.+|++|- T Consensus 278 ~~pV~i~~~~----~~~---~~~~gl~~G~~vv 303 (304) T pfam00529 278 GVPVEIGLDP----AFN---QSTTPLVPGEVVI 303 (304) T ss_pred EEEEEEEEEC----CCC---HHCCCCCCCCEEE T ss_conf 6899999827----833---3126989998897 No 87 >TIGR01349 PDHac_trf_mito pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase; InterPro: IPR006257 This group of sequences represent one of several closely related clades of the dihydrolipoamide acetyltransferase subunit of the pyruvate dehydrogenase complex. It includes sequences from mitochondria and from alpha and beta branches of the proteobacteria, as well as from some other bacteria, but not the Gram-positive bacteria.; GO: 0004742 dihydrolipoyllysine-residue acetyltransferase activity, 0006090 pyruvate metabolic process, 0045254 pyruvate dehydrogenase complex. Probab=64.05 E-value=6.3 Score=18.30 Aligned_cols=13 Identities=31% Similarity=0.378 Sum_probs=6.7 Q ss_pred CCCEEECCCCCCC Q ss_conf 4200302679672 Q gi|254780879|r 513 HTGVDWAAPRGTP 525 (652) Q Consensus 513 H~GVD~aAp~GTP 525 (652) |+=||++...=|| T Consensus 441 y~~vDiSVAVatP 453 (584) T TIGR01349 441 YKNVDISVAVATP 453 (584) T ss_pred ECEEEEEEEEECC T ss_conf 1201488776568 No 88 >PRK09507 cspE cold shock protein CspE; Reviewed Probab=63.85 E-value=9.5 Score=17.07 Aligned_cols=33 Identities=30% Similarity=0.345 Sum_probs=24.9 Q ss_pred CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHH Q ss_conf 967999653089700799983997488200214454 Q gi|254780879|r 531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIA 566 (652) Q Consensus 531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a 566 (652) .|+|.+-.-..|||-.. -.+|=.-.|-|.|.+. T Consensus 5 ~G~VKwF~~~kGyGFI~---~~dG~~DvFvH~s~i~ 37 (69) T PRK09507 5 KGNVKWFNESKGFGFIT---PEDGSKDVFVHFSAIQ 37 (69) T ss_pred EEEEEEEECCCCEEEEE---CCCCCCCEEEEHHHCC T ss_conf 88999983999879997---0799832999907705 No 89 >PRK09578 periplasmic multidrug efflux lipoprotein precursor; Reviewed Probab=63.64 E-value=5.4 Score=18.77 Aligned_cols=14 Identities=7% Similarity=0.147 Sum_probs=6.9 Q ss_pred HHHHHHHHHHHHCC Q ss_conf 99999999876268 Q gi|254780879|r 54 GVIIGGSLLTALDG 67 (652) Q Consensus 54 ~~l~g~a~~~aldg 67 (652) ++||+..+.++... T Consensus 12 ~~l~~~~~L~gC~~ 25 (385) T PRK09578 12 AALVAAFALAGCGK 25 (385) T ss_pred HHHHHHHHHHCCCC T ss_conf 99999999816799 No 90 >PRK09859 multidrug efflux system protein MdtE; Provisional Probab=63.25 E-value=5.9 Score=18.50 Aligned_cols=13 Identities=38% Similarity=0.675 Sum_probs=5.8 Q ss_pred HHHHHHHHHHHCC Q ss_conf 9999999876268 Q gi|254780879|r 55 VIIGGSLLTALDG 67 (652) Q Consensus 55 ~l~g~a~~~aldg 67 (652) +|+.++++++..+ T Consensus 11 ll~~~~lL~gC~~ 23 (385) T PRK09859 11 LLFCGAMLTACDD 23 (385) T ss_pred HHHHHHHHHCCCC T ss_conf 9999999953799 No 91 >pfam05651 Diacid_rec Putative sugar diacid recognition. This region is found in several proteins characterized as carbohydrate diacid regulators. An HTH DNA-binding motif is found at the C-terminus of these proteins suggesting that this region includes the sugar recognition region. Probab=62.94 E-value=5.7 Score=18.65 Aligned_cols=60 Identities=25% Similarity=0.342 Sum_probs=36.1 Q ss_pred CCCCEEEEEEEECCCC-----CEEEEECCCCEEEEEHHHHHHHHCCCCCC---EEECCCEEEEECCCCC Q ss_conf 1596799965308970-----07999839974882002144541188997---8834958998416678 Q gi|254780879|r 529 VGDGIVEKANWAGGYG-----KQTLIHHGNGYVSSYNHQDAIAKNIKAGT---AVKQGQIIGWIGTTGL 589 (652) Q Consensus 529 ag~G~V~~ag~~~GyG-----n~V~I~H~~Gy~T~YaHlS~~a~gV~~G~---~V~qGQvIG~vGsTG~ 589 (652) -.+|+++.+|...=-| =.-.|+++.. ...|.....-.+|+|+|- -+-+|++||-+|-||- T Consensus 25 d~~G~IIAS~d~~RiG~~HegA~~vi~~~~~-~~i~~~~~~~~~G~k~GiNlPi~~~g~viGvIGITG~ 92 (135) T pfam05651 25 DEQGVIIASGDPSRIGQFHEGALLALREGRV-VEIDAADASRLKGVKPGINLPIIFQGEVIGVIGITGE 92 (135) T ss_pred CCCCEEEECCCHHHCCCHHHHHHHHHHCCCE-EEECHHHHHHCCCCCCCCEECEEECCEEEEEEEEECC T ss_conf 9997799608856572232999999973991-8985767744579887512586989999999996289 No 92 >cd06850 biotinyl_domain The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase, oxaloacetate decarboxylase, methylmalonyl-CoA decarboxylase, transcarboxylase and urea amidolyase. This domain functions in transferring CO2 from one subsite to another, allowing carboxylation, decarboxylation, or transcarboxylation. During this process, biotin is covalently attached to a specific lysine. Probab=62.12 E-value=5.9 Score=18.55 Aligned_cols=20 Identities=25% Similarity=0.421 Sum_probs=15.3 Q ss_pred CCCCCEEECCCEEEEECCCC Q ss_conf 88997883495899841667 Q gi|254780879|r 569 IKAGTAVKQGQIIGWIGTTG 588 (652) Q Consensus 569 V~~G~~V~qGQvIG~vGsTG 588 (652) |+.|++|+.||+++.+-+-- T Consensus 15 V~~Gd~V~~G~~l~~iE~mK 34 (67) T cd06850 15 VKEGDKVEAGQPLAVLEAMK 34 (67) T ss_pred ECCCCEECCCCEEEEEEECC T ss_conf 57999997899999999366 No 93 >PRK05035 electron transport complex protein RnfC; Provisional Probab=62.05 E-value=4.9 Score=19.10 Aligned_cols=14 Identities=21% Similarity=0.109 Sum_probs=5.9 Q ss_pred CCHHHHHHHHCCCC Q ss_conf 65033443202333 Q gi|254780879|r 204 AQDEEIKNAIMNQF 217 (652) Q Consensus 204 ~~~~~~~~~~~~~~ 217 (652) ++.++....+++.+ T Consensus 131 ~~~~el~~~I~~AG 144 (725) T PRK05035 131 LSREELIERIRQAG 144 (725) T ss_pred CCHHHHHHHHHHCC T ss_conf 89999999999759 No 94 >cd06165 Sortase_A_1 Sortase A (SrtA) or subfamily-1 sortases are cysteine transpeptidases found in gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal (usually a pentapeptide motif), and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. This group contains a subset of Class A (subfamily-1) sortases, excluding SrtA from Staphylococcus aureus. Sortase A cleaves between threonine and glycine of the LPXTG motif in a wide range of protein substrates. It affects the ability of a pathogen to establish successful infection. Sortase A contains an N-terminal region that functions as both a signal peptide for secretion and a stop-tra Probab=60.43 E-value=5.8 Score=18.59 Aligned_cols=56 Identities=20% Similarity=0.278 Sum_probs=33.6 Q ss_pred CCCCCEEEEECCCCE-EEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCCCCEEEEEEEECCEECCCCEEC Q ss_conf 897007999839974-882002144541188997883495899841667888742688997867883662000 Q gi|254780879|r 541 GGYGKQTLIHHGNGY-VSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVNGIKVDSTKVR 612 (652) Q Consensus 541 ~GyGn~V~I~H~~Gy-~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vnG~~VdP~~~~ 612 (652) .|-||+|+--|..++ -+.+.+|.. +++|+.| ++-+.+ --..|+|... .-|+|-.+. T Consensus 39 ~G~gN~viaGH~~~~~~~~F~~L~~----l~~GD~I-------~v~~~~----~~~~Y~V~~~-~iV~p~d~~ 95 (127) T cd06165 39 MGKGNYALAGHNMRNKGVLFSPLYK----VKVGDKI-------YLTDKD----NVYEYKVTSK-KIVDPTRVD 95 (127) T ss_pred CCCCCEEEEECCCCCCCCCCCCHHH----CCCCCEE-------EEEECC----CEEEEEEEEE-EEECCCCCE T ss_conf 9988699993658867654667656----8999999-------999899----3999999489-999988777 No 95 >PRK11556 multidrug efflux system subunit MdtA; Provisional Probab=59.89 E-value=7.1 Score=17.94 Aligned_cols=19 Identities=11% Similarity=0.263 Sum_probs=8.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 899989899999999999999987 Q gi|254780879|r 40 LRWLSTTFFAGITSGVIIGGSLLT 63 (652) Q Consensus 40 ~rw~~~t~ltg~~~~~l~g~a~~~ 63 (652) +|||.-.++ .+++|++.|- T Consensus 7 ~~~~~~~~~-----~~~~~~~~~~ 25 (415) T PRK11556 7 FRWVIVIVV-----VIAAIAAFWF 25 (415) T ss_pred HHHHHHHHH-----HHHHHHHHHH T ss_conf 589999999-----9999999987 No 96 >PRK10559 p-hydroxybenzoic acid efflux subunit AaeA; Provisional Probab=56.29 E-value=13 Score=16.19 Aligned_cols=14 Identities=7% Similarity=0.105 Sum_probs=7.8 Q ss_pred CHHHCCCCCEEEEE Q ss_conf 61016998889999 Q gi|254780879|r 313 RVDQLTKDEILRIG 326 (652) Q Consensus 313 ~~~~Lr~Gq~L~I~ 326 (652) .+..+++||...|. T Consensus 201 qL~~ir~Gq~v~I~ 214 (310) T PRK10559 201 KLEGVRPGYRAEIT 214 (310) T ss_pred HCCCCCCCCEEEEE T ss_conf 12538999979999 No 97 >COG1155 NtpA Archaeal/vacuolar-type H+-ATPase subunit A [Energy production and conversion] Probab=55.78 E-value=9.3 Score=17.15 Aligned_cols=26 Identities=23% Similarity=0.176 Sum_probs=18.8 Q ss_pred ECCCCCHHHHHHHCCCCHHHHHHHHH Q ss_conf 41797089999974999899999999 Q gi|254780879|r 281 IQHNTTIFDAMVHAGYSNGDSAKIAK 306 (652) Q Consensus 281 VK~GDTL~~IL~r~Gvs~~ei~~i~~ 306 (652) |--|.|+..-.++.|++..-.+.-.. T Consensus 306 IYtGiTiaEY~RDmGy~v~lmADSTS 331 (588) T COG1155 306 IYTGITIAEYYRDMGYDVALMADSTS 331 (588) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCHHH T ss_conf 53223199988763025677501389 No 98 >TIGR01846 type_I_sec_HlyB type I secretion system ATPase; InterPro: IPR010132 Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This entry contains one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N terminus, but rather carry signals located toward the extreme C terminus to direct type I secretion.; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0015031 protein transport, 0016021 integral to membrane. Probab=55.70 E-value=5.9 Score=18.51 Aligned_cols=137 Identities=14% Similarity=0.098 Sum_probs=78.6 Q ss_pred EEEEECCCC-CHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEE-CCCCCCCEEEEE--EECCCCCEEEEEE Q ss_conf 368841797-089999974999899999999854015610169988899997-278886405899--9716883489998 Q gi|254780879|r 277 DLIPIQHNT-TIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGV-VQKDDKFTIVRF--SIYHKQKHLLTIA 352 (652) Q Consensus 277 ~~v~VK~GD-TL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~-~~~~~~~~~~r~--si~~~~~~~~~va 352 (652) -.++..+|+ ++..|=-||.=+..++-. ..++ .|++|+.|=|.. +.+| +.++.++ .+|.-..-.+.+. T Consensus 455 aalP~l~G~i~F~nirFRY~pD~PeVL~-------nl~L-~I~~Ge~IGIvGpSGSG-KSTLTKL~QRLYtP~~GqVLVD 525 (703) T TIGR01846 455 AALPELKGSITFENIRFRYKPDSPEVLS-------NLSL-DIKPGEVIGIVGPSGSG-KSTLTKLLQRLYTPEHGQVLVD 525 (703) T ss_pred CCCCCCCCCEEEEEEEECCCCCCCHHHH-------CCCC-CCCCCEEEEEECCCCCC-HHHHHHHHHHHCCCCCCEEEEC T ss_conf 0354225726787533146888717873-------2687-65786579987278986-7899999886148888747770 Q ss_pred ECCCCCEEECCCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHCCCCCEEEE Q ss_conf 42788432013332100000122111233454211025666887199989999999973011101210144540688 Q gi|254780879|r 353 LNDNNEYVLGVEPVKMDINHQMDYMRTSEESPNIYDGIWRATSFNGMNSNLVKLIMRTLASSVNLQEHLKPTDFLET 429 (652) Q Consensus 353 ~~d~g~fv~~~ep~~~~~~~~~~~~~~~~~~~~I~~SLy~aa~~~gip~~ii~~lv~i~a~dVDFqr~ir~GD~f~V 429 (652) --|-. -.+|....++.-..--........|.|+|. ..+-++|..-+--.++ ++---||...++.|=.-+| T Consensus 526 G~DLA----~~DP~wLRRQ~gVVLQEn~LFsrSirdNI~--l~~P~~~~E~Vi~AA~-LAGA~dFI~~Lp~GY~T~v 595 (703) T TIGR01846 526 GVDLA----IADPAWLRRQVGVVLQENVLFSRSIRDNIA--LCNPGASVEHVIAAAK-LAGAHDFISELPQGYNTEV 595 (703) T ss_pred CCCCC----CCCCCHHHHCCEEEEECCHHHCCCHHHHHH--HCCCCCCHHHHHHHHH-HCCHHHHHHHCCCCCCCCC T ss_conf 30001----018520102230234000210122788985--1777769899999986-2185899973637677400 No 99 >PRK10218 GTP-binding protein; Provisional Probab=54.93 E-value=12 Score=16.27 Aligned_cols=43 Identities=26% Similarity=0.417 Sum_probs=34.8 Q ss_pred CEEEEECCCCEEEEEHHHHHHHHC---CCCCCEEECCCEEEEECCC Q ss_conf 079998399748820021445411---8899788349589984166 Q gi|254780879|r 545 KQTLIHHGNGYVSSYNHQDAIAKN---IKAGTAVKQGQIIGWIGTT 587 (652) Q Consensus 545 n~V~I~H~~Gy~T~YaHlS~~a~g---V~~G~~V~qGQvIG~vGsT 587 (652) |=+.|-+.+|-.|.|+-.+--.+| |.+|..|=.|+|||.---. T Consensus 485 ~G~lis~~~g~~t~yal~~lq~rg~lfv~pg~~vy~GmivGe~~r~ 530 (607) T PRK10218 485 NGVLISNGQGKAVAFALFGLQDRGKLFLGHGAEVYEGQIIGIHSRS 530 (607) T ss_pred CEEEEECCCCEEHHHHHHHHHHCCCEEECCCCCEECCEEEEEECCC T ss_conf 5137975776178987753875453673699966887586760786 No 100 >cd06663 Biotinyl_lipoyl_domains Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl, or methylamine, respectively, between components of the complex/protein via a biotinyl or lipoyl group, which is covalently attached to a highly conserved lysine residue. Probab=53.93 E-value=9.9 Score=16.93 Aligned_cols=17 Identities=35% Similarity=0.556 Sum_probs=7.7 Q ss_pred CCCCCEEECCCEEEEEC Q ss_conf 88997883495899841 Q gi|254780879|r 569 IKAGTAVKQGQIIGWIG 585 (652) Q Consensus 569 V~~G~~V~qGQvIG~vG 585 (652) +++|++|++||.+..+= T Consensus 21 v~~Gd~V~~Gd~l~~iE 37 (73) T cd06663 21 KKVGDKVKKGDVLAEIE 37 (73) T ss_pred ECCCCEECCCCEEEEEE T ss_conf 26999997999999999 No 101 >pfam00364 Biotin_lipoyl Biotin-requiring enzyme. This family covers two Prosite entries, the conserved lysine residue binds biotin in one group and lipoic acid in the other. Note that the model may not recognize the Glycine cleavage system H proteins. Probab=53.88 E-value=9.9 Score=16.93 Aligned_cols=18 Identities=33% Similarity=0.571 Sum_probs=9.1 Q ss_pred CCCCCEEECCCEEEEECC Q ss_conf 889978834958998416 Q gi|254780879|r 569 IKAGTAVKQGQIIGWIGT 586 (652) Q Consensus 569 V~~G~~V~qGQvIG~vGs 586 (652) +++|+.|++||.|..+-+ T Consensus 21 v~~Gd~V~~g~~l~~iEt 38 (73) T pfam00364 21 VKVGDKVKAGQVLCEVEA 38 (73) T ss_pred ECCCCEECCCCEEEEEEE T ss_conf 589899928998999996 No 102 >TIGR02472 sucr_P_syn_N sucrose-phosphate synthase, putative, glycosyltransferase domain; InterPro: IPR012822 This family consists of the N-terminal regions, or in some cases the entirety, of bacterial proteins closely related to plant sucrose-phosphate synthases (SPS). The C-terminal domain (IPR012821 from INTERPRO), found with most members of this family, resembles both bona fide plant sucrose-phosphate phosphatases (SPP) and the SPP-like domain of plant sucrose phosphate synthase (SPS). At least two members of this family lack the SPP-like domain, which may have binding or regulatory rather than enzymatic activity by analogy to plant SPS. This enzyme produces sucrose 6-phosphate and UDP from UDP-glucose and D-fructose 6-phosphate, and may be encoded near the gene for fructokinase.. Probab=51.86 E-value=5.2 Score=18.94 Aligned_cols=26 Identities=46% Similarity=0.607 Sum_probs=20.1 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEECCCC Q ss_conf 102356764143404434642003026796727971596 Q gi|254780879|r 494 RMTSGFGMRYHPILGYSRMHTGVDWAAPRGTPIVAVGDG 532 (652) Q Consensus 494 risS~Fg~R~hPilg~~r~H~GVD~aAp~GTPI~Aag~G 532 (652) -+|-|||--. ==||.+|=||+|+.|| T Consensus 354 ALTEPFGLTL-------------lEAAAcGLPivAT~DG 379 (445) T TIGR02472 354 ALTEPFGLTL-------------LEAAACGLPIVATEDG 379 (445) T ss_pred CCCCCCHHHH-------------HHHHHCCCCEEECCCC T ss_conf 2125301689-------------9999769972107864 No 103 >cd06166 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5, represented by Clostridium perfringens CPE2315. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell. Probab=51.59 E-value=9.7 Score=16.99 Aligned_cols=81 Identities=20% Similarity=0.209 Sum_probs=39.2 Q ss_pred CEEECCCCCCCEEECCCCEEEEEEEE--CCCCCEEEEECCCCE-EEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCC Q ss_conf 00302679672797159679996530--897007999839974-882002144541188997883495899841667888 Q gi|254780879|r 515 GVDWAAPRGTPIVAVGDGIVEKANWA--GGYGKQTLIHHGNGY-VSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLST 591 (652) Q Consensus 515 GVD~aAp~GTPI~Aag~G~V~~ag~~--~GyGn~V~I~H~~Gy-~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~ST 591 (652) ++++..-.||-=.+-..|...+.+.. |..||+|+--|...+ -+.+.||.+ +++|++|. . .++.. T Consensus 12 ~~~~pi~~g~~~~~L~~G~g~~~~t~~PG~~gN~viaGH~~~~~~~~F~~L~~----l~~GD~I~------l--~~~~~- 78 (126) T cd06166 12 DLKLPILEGTDEENLKYALGHFENTAMPGENGNFAIAGHRSYTYGRIFNRLDE----VEKGDEIK------V--TTKNG- 78 (126) T ss_pred CCEEEEEECCCHHHHHCCCEEECCCCCCCCCCCEEEEEEECCCCCCCCCCHHH----CCCCCEEE------E--EECCE- T ss_conf 98868994899899812657623888899996299997508887855200551----85899999------9--99998- Q ss_pred CCEEEEEEEECCEECCCCEE Q ss_conf 74268899786788366200 Q gi|254780879|r 592 GPHLHYELIVNGIKVDSTKV 611 (652) Q Consensus 592 GPHLHfEv~vnG~~VdP~~~ 611 (652) -.+|+|... +-|+|-.+ T Consensus 79 --~y~Y~V~~~-~iV~p~d~ 95 (126) T cd06166 79 --TYKYKITSI-FVVEPTDT 95 (126) T ss_pred --EEEEEEEEE-EEECCCCC T ss_conf --999999779-99997655 No 104 >pfam02241 MCR_beta Methyl-coenzyme M reductase beta subunit, C-terminal domain. Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (pfam02249), 2 beta (this family), and 2 gamma (pfam2240) subunits with two identical nickel porphinoid active sites. The C-terminal domain of MCR beta has an all-alpha fold with buried central helix. Probab=50.93 E-value=13 Score=16.18 Aligned_cols=46 Identities=20% Similarity=0.200 Sum_probs=28.9 Q ss_pred CCCCCEEECCCCCCCEEECCCCEEEEEEEE-C-CCCCEEEEECCCCEE Q ss_conf 464200302679672797159679996530-8-970079998399748 Q gi|254780879|r 511 RMHTGVDWAAPRGTPIVAVGDGIVEKANWA-G-GYGKQTLIHHGNGYV 556 (652) Q Consensus 511 r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~-~-GyGn~V~I~H~~Gy~ 556 (652) .---|+||.-..||-|--.-=---||-|-. | -+||.|+-||..|+- T Consensus 155 TgLPg~D~Gr~~GtaVgfSFFSHSIYGGGGPGiFnGNHvVTRHskG~a 202 (255) T pfam02241 155 TGLPGVDFGRAEGTAVGFSFFSHSIYGGGGPGIFHGNHIVTRHSKGFA 202 (255) T ss_pred CCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCCEEEEECCCCCC T ss_conf 289986554202225322311001005898865148757884478732 No 105 >PRK03140 phosphatidylserine decarboxylase; Provisional Probab=50.09 E-value=16 Score=15.53 Aligned_cols=35 Identities=14% Similarity=0.027 Sum_probs=20.3 Q ss_pred HHHHHHHCCCCHHHHHHHHH---HHHCCCCHHHCCCCCE Q ss_conf 89999974999899999999---8540156101699888 Q gi|254780879|r 287 IFDAMVHAGYSNGDSAKIAK---ALKNEVRVDQLTKDEI 322 (652) Q Consensus 287 L~~IL~r~Gvs~~ei~~i~~---al~~~~~~~~Lr~Gq~ 322 (652) +-.-.+.++++-+|+.+=+. +++..+ .++|++|.+ T Consensus 35 I~~fik~~~In~~E~~~~~~~Y~sfndFF-tR~Lk~g~R 72 (259) T PRK03140 35 IPSYAKVFQINQDEMEKGLKEYRTLHELF-TRKLKEGKR 72 (259) T ss_pred HHHHHHHHCCCHHHHHCCHHHCCCHHHHH-HCCCCCCCC T ss_conf 99999997979899636964489889962-104678986 No 106 >PRK03934 phosphatidylserine decarboxylase; Provisional Probab=49.38 E-value=7.2 Score=17.93 Aligned_cols=17 Identities=59% Similarity=0.812 Sum_probs=13.1 Q ss_pred CCCCCCEEECCCEEEEE Q ss_conf 18899788349589984 Q gi|254780879|r 568 NIKAGTAVKQGQIIGWI 584 (652) Q Consensus 568 gV~~G~~V~qGQvIG~v 584 (652) .+++|++|+.||.||.+ T Consensus 250 ~l~~g~~Vk~Gq~ig~~ 266 (267) T PRK03934 250 NLKAGESVKFGESIGKI 266 (267) T ss_pred CCCCCCEEEEEHHHCCC T ss_conf 67899998820432014 No 107 >TIGR03257 met_CoM_red_bet methyl-coenzyme M reductase, beta subunit. Members of this protein family are the beta subunit of methyl coenzyme M reductase, also called coenzyme-B sulfoethylthiotransferase (EC 2.8.4.1). This enzyme, with alpha, beta, and gamma subunits, catalyzes the last step in methanogenesis. Several methanogens have encode two such enzymes, designated I and II; this model does not separate the isozymes. Probab=49.28 E-value=13 Score=16.01 Aligned_cols=51 Identities=22% Similarity=0.214 Sum_probs=31.0 Q ss_pred CCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEE-C-CCCCEEEEECCCCEE Q ss_conf 40443464200302679672797159679996530-8-970079998399748 Q gi|254780879|r 506 ILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWA-G-GYGKQTLIHHGNGYV 556 (652) Q Consensus 506 ilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~-~-GyGn~V~I~H~~Gy~ 556 (652) ++-+-.---|+||.-..||-|--.-=---||-|-. | -+||+|+-||..|+- T Consensus 334 llE~ETGLPG~D~Gr~~GtaVgfSFFSHSIYGGGGPGiFnGNHVVTRHskG~a 386 (433) T TIGR03257 334 ILEKETGLPGVDYGRVEGTAVGFSFFSHSIYGGGGPGIFNGNHVVTRHSKGFA 386 (433) T ss_pred HHHHHCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCEEEEECCCCCC T ss_conf 56661289987555412135423310002106898865058757883478732 No 108 >pfam10262 Rdx Rdx family. This entry is an approximately 100 residue region of selenoprotein-T, conserved from plants to humans. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins, including selenoprotein T. However, despite its binding to UGTR and that its mRNA is up-regulated in extended asphyxia, the function of the protein and hence of this region of it is unknown. Selenoprotein W contains selenium as selenocysteine in the primary protein structure and levels of this selenoprotein are affected by selenium. Probab=48.91 E-value=16 Score=15.40 Aligned_cols=54 Identities=19% Similarity=0.112 Sum_probs=35.1 Q ss_pred EEEEEC--CCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCCCCEEEEEEEECCEECCCC Q ss_conf 799983--9974882002144541188997883495899841667888742688997867883662 Q gi|254780879|r 546 QTLIHH--GNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVNGIKVDST 609 (652) Q Consensus 546 ~V~I~H--~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vnG~~VdP~ 609 (652) .|.|.+ ..||..+|..|+..... +-++.+ .++-...|++| -|||.+||.-|=-. T Consensus 2 ~V~I~YC~~Cg~~~ra~~l~qeLl~-~f~~~i--~~v~l~p~~~G-------~FeV~v~~~li~sk 57 (76) T pfam10262 2 KVTIEYCTQCGWLLRAAWLAQELLS-TFPDDL--IEVELQPGTGG-------AFEVTVNGELIWSK 57 (76) T ss_pred EEEEEECCCCCCHHHHHHHHHHHHH-HCCCHH--HEEEEEECCCC-------EEEEEECCEEEEEE T ss_conf 1899987888981899999999998-776400--15886647993-------59999999998983 No 109 >cd00004 Sortase Sortases are cysteine transpeptidases, found in gram-positive bacteria, that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The different classes are called Sortase A or SrtA (subfamily 1), B or SrtB (subfamily 2), C or SrtC (subfamily3), D or SrtD (subfamilies 4 and 5), and E or SrtE. In two different sortase subfamilies, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one s Probab=48.79 E-value=11 Score=16.55 Aligned_cols=31 Identities=23% Similarity=0.462 Sum_probs=17.9 Q ss_pred CCCCCEEEEECCCCE-EEEEHHHHHHHHCCCCCCEE Q ss_conf 897007999839974-88200214454118899788 Q gi|254780879|r 541 GGYGKQTLIHHGNGY-VSSYNHQDAIAKNIKAGTAV 575 (652) Q Consensus 541 ~GyGn~V~I~H~~Gy-~T~YaHlS~~a~gV~~G~~V 575 (652) |.-||+|+--|..++ .+.+.+|.. +++|+.| T Consensus 40 g~~gN~vIaGH~~~~~~~~F~~L~~----l~~GD~i 71 (128) T cd00004 40 GENGNTVIAGHRGGDSGTVFSDLDN----LKKGDKI 71 (128) T ss_pred CCCCCEEEEEEECCCCCCCCCCHHH----CCCCCEE T ss_conf 9996099999818998844365545----7689989 No 110 >KOG3962 consensus Probab=48.78 E-value=16 Score=15.39 Aligned_cols=71 Identities=21% Similarity=0.254 Sum_probs=35.8 Q ss_pred CCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCCC Q ss_conf 64200302679672797159679996530897007999839974882002144541188997883495899841667 Q gi|254780879|r 512 MHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTG 588 (652) Q Consensus 512 ~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG 588 (652) +|.-+| .|--++|+++-.=-=-.+.-.+|||+|+-|.- +|.+ |+-...+. .-..+.-|-|++-.+.+-|+| T Consensus 73 ph~~~~--gp~p~e~f~avki~dsrIaLKsGyGKYlsins-dglv--vg~qeAvG-~~EQw~~vFq~~r~a~~as~s 143 (246) T KOG3962 73 PHDEVD--GPEPEEQFMAVKISDSRIALKSGYGKYLSINS-DGLV--VGRQEAVG-SREQWEPVFQEGRMALLASNS 143 (246) T ss_pred CCCCCC--CCCCCHHEEEEECCCCEEEEECCCCCEEEECC-CCCE--EEEHHHCC-CHHHCHHHHHCCCEEEEECCC T ss_conf 775456--89971007999736864773046551566547-7637--87434318-565330134236267663266 No 111 >cd05828 Sortase_D_4 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-4. These sortases recognize a unique sorting signal (LPXTA) and they constitute a specialized sorting pathway found in bacilli. Their substrates are predicted to be predominantly enzymes such as 5'-nucleotidases, glycosyl hydrolase, and subtilase. Probab=48.52 E-value=10 Score=16.76 Aligned_cols=14 Identities=21% Similarity=0.335 Sum_probs=8.2 Q ss_pred CCCCCEEEEECCCC Q ss_conf 89700799983997 Q gi|254780879|r 541 GGYGKQTLIHHGNG 554 (652) Q Consensus 541 ~GyGn~V~I~H~~G 554 (652) |.-||+|+--|.+. T Consensus 41 G~~GN~viaGH~~~ 54 (127) T cd05828 41 GEGGNIVIAGHRDT 54 (127) T ss_pred CCCCCEEEEEECCC T ss_conf 98886999950688 No 112 >PRK05889 putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Provisional Probab=48.06 E-value=13 Score=16.02 Aligned_cols=16 Identities=25% Similarity=0.638 Sum_probs=11.6 Q ss_pred CCCCCEEECCCEEEEE Q ss_conf 8899788349589984 Q gi|254780879|r 569 IKAGTAVKQGQIIGWI 584 (652) Q Consensus 569 V~~G~~V~qGQvIG~v 584 (652) +++|+.|..||++..+ T Consensus 55 v~~Gd~V~~Gd~L~~I 70 (71) T PRK05889 55 VSVGDVIQAGDLIAVI 70 (71) T ss_pred ECCCCEECCCCEEEEE T ss_conf 7899998899999996 No 113 >pfam10165 Ric8 Guanine nucleotide exchange factor synembryn. Ric8 is involved in the EGL-30 neurotransmitter signalling pathway. It is a guanine nucleotide exchange factor that regulates neurotransmitter secretion. Probab=47.56 E-value=6 Score=18.49 Aligned_cols=84 Identities=10% Similarity=0.092 Sum_probs=43.4 Q ss_pred EEEHHHHHHHHCCCCCCEEECCCEEEEECC-CCCCCCCEEEEEEEECCEECCCCEE-CCCC--CCCCCHHHHHHHHHHHH Q ss_conf 820021445411889978834958998416-6788874268899786788366200-0788--78788899999999999 Q gi|254780879|r 557 SSYNHQDAIAKNIKAGTAVKQGQIIGWIGT-TGLSTGPHLHYELIVNGIKVDSTKV-RIPE--RENLKGDLLQRFAMEKK 632 (652) Q Consensus 557 T~YaHlS~~a~gV~~G~~V~qGQvIG~vGs-TG~STGPHLHfEv~vnG~~VdP~~~-~lp~--~~~l~~~~l~~F~~~~~ 632 (652) |-|+|.++|. .+.|--.-++-.-+|... ++..|.+- ...+..|||.+= ..|. ..++++ |.+=+||++ T Consensus 337 ~GYGnAAGlL--a~rgll~~~~~~~~ySsd~edsdteey-----~~~~~~INPVTG~~~~~e~~n~~~~--MTeEeKE~E 407 (438) T pfam10165 337 IGYGNAAGLL--ANRGLLGPGRAQEAYSSDSEDSDTEEY-----KSAKRAINPITGQVEDAEKPNPMEG--MTEEEKERE 407 (438) T ss_pred CCCHHHHHHH--HHCCCCCCCCCCCCCCCCCCCCCHHHH-----HHCCCCCCCCCCCCCCCCCCCCCCC--CCHHHHHHH T ss_conf 4851789999--874887887654234678776530456-----6406777987687678778999887--898899999 Q ss_pred --HHHHHHHCCC-----CCCCCEE Q ss_conf --9999984147-----7667534 Q gi|254780879|r 633 --RINSLLNNGE-----NPKKPLF 649 (652) Q Consensus 633 --~id~ll~~~~-----~~~~~~~ 649 (652) |+-.|+++.. .|..|+. T Consensus 408 AerL~~LfdrL~~~GvIq~~npv~ 431 (438) T pfam10165 408 AERLFVLFERLKKTGVVQVENPVA 431 (438) T ss_pred HHHHHHHHHHHHHCCCCCCCCHHH T ss_conf 999999999998669767886688 No 114 >PRK04599 consensus Probab=47.46 E-value=14 Score=15.81 Aligned_cols=32 Identities=9% Similarity=0.254 Sum_probs=20.9 Q ss_pred CCCEEEEEHH-HHHHHHCCCCCCEEECCCEEEE Q ss_conf 9974882002-1445411889978834958998 Q gi|254780879|r 552 GNGYVSSYNH-QDAIAKNIKAGTAVKQGQIIGW 583 (652) Q Consensus 552 ~~Gy~T~YaH-lS~~a~gV~~G~~V~qGQvIG~ 583 (652) |...+..+.- .-++...+++|++|+-||.||. T Consensus 251 GSTVIllF~~~~~~~~~~l~~g~~vrmGq~la~ 283 (285) T PRK04599 251 GSTVINLFAKDAIRFDESMANGQPTRMGTPYAH 283 (285) T ss_pred CCEEEEEECCCCCCCCHHCCCCCEEECCCCCCC T ss_conf 884999926998551000688998751831015 No 115 >TIGR01394 TypA_BipA GTP-binding protein TypA; InterPro: IPR006298 This bacterial (and Arabidopsis) protein, termed TypA or BipA, is a GTP-binding protein. It is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways, but the precise function is unknown.; GO: 0005525 GTP binding, 0005622 intracellular. Probab=46.67 E-value=17 Score=15.29 Aligned_cols=199 Identities=18% Similarity=0.212 Sum_probs=89.1 Q ss_pred HHHHH-HHCCCCHHHHHHHHHHHCCCCHHHH-HCCCCCEEE----------EEEEEECCCCC--CCCCCCEEEEEEECCC Q ss_conf 56668-8719998999999997301110121-014454068----------87532115785--1246723688962388 Q gi|254780879|r 390 IWRAT-SFNGMNSNLVKLIMRTLASSVNLQE-HLKPTDFLE----------TFFSVNHANNQ--ASDDSELLYIHARFGE 455 (652) Q Consensus 390 Ly~aa-~~~gip~~ii~~lv~i~a~dVDFqr-~ir~GD~f~----------Vlye~~~~~g~--~~~~geil~A~~~~~g 455 (652) |+..- -+.--+..+-.+|.+-+..+|-..- +...-|.|+ |+.|.+-.+|- .++.+++.|-. ..| T Consensus 326 lAG~EVGk~VTSR~i~dRL~rEL~~NvALrVe~t~~~D~f~VsGRGELhLsILiEtMRREGfEl~Vg~P~Vi~k~--~dG 403 (609) T TIGR01394 326 LAGKEVGKFVTSRQIRDRLERELETNVALRVEDTESADKFEVSGRGELHLSILIETMRREGFELQVGRPQVIYKE--IDG 403 (609) T ss_pred CCCCCCCCEECCCCHHHHHHHHHHCCCEEEEECCCCCCCEEEECCEEEHHHHHHHCCCCCCEEEEECCCEEEEEE--ECC T ss_conf 655325730324415789999863171456403898873487201113023454203444414753597789984--588 Q ss_pred CCCCCCCCCCCC--CCCCCCCCCCCCCHHHCCCC--CCCCC-CCCCCCCC-CCCCCCCCCCCCCCCEEECCCCCCCEEEC Q ss_conf 542013455766--55444335566100000112--33345-41023567-64143404434642003026796727971 Q gi|254780879|r 456 TRTRFYRFLNPV--DGSVEYFNENGKSSRPFLLR--TPVPF-GRMTSGFG-MRYHPILGYSRMHTGVDWAAPRGTPIVAV 529 (652) Q Consensus 456 ~~~~~yrf~~~~--~~~~~yyd~~G~S~~k~llr--~Pv~~-~risS~Fg-~R~hPilg~~r~H~GVD~aAp~GTPI~Aa 529 (652) +....|-.-+-+ +...+.. -+--+.||+-|. .|... ||++=-|- +-| ...|| .+-=...-+||=|+.. T Consensus 404 ~k~EP~E~~~IDVPEe~~G~V-~e~Lg~RKgEm~~M~~~g~EG~tRl~F~~PsR-GLIGf----r~~FlT~TrG~Gimn~ 477 (609) T TIGR01394 404 KKLEPIEELTIDVPEEHVGAV-IEKLGKRKGEMKDMEPSGNEGRTRLEFVIPSR-GLIGF----RTEFLTDTRGTGIMNH 477 (609) T ss_pred EEECCEEEEEEECCCCCCCHH-HHHHCCCCEEEEECCCCCCCCEEEEEEECCCC-CHHHH----HHHHHHHHHHHHHHHH T ss_conf 531875699980285335466-65314783477725676996469999981664-00122----0245441021311201 Q ss_pred CCCEEEEEEEE-C---CCCCEEEEECCCCEEEEEHHHHHHHHC---CCCCCEEECCCEEEEECCCCCCCCCEEEEEEEEC Q ss_conf 59679996530-8---970079998399748820021445411---8899788349589984166788874268899786 Q gi|254780879|r 530 GDGIVEKANWA-G---GYGKQTLIHHGNGYVSSYNHQDAIAKN---IKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVN 602 (652) Q Consensus 530 g~G~V~~ag~~-~---GyGn~V~I~H~~Gy~T~YaHlS~~a~g---V~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vn 602 (652) - =-.|.=|. | .-=|=+.|--.+|-.|.||=+|-=-|| |.+|++|=+|+|||-== |-| T Consensus 478 ~--F~~Y~P~~pG~i~~R~~GsLVs~~~G~a~~YaL~nLqeRG~~Fv~pG~~VY~GMIiGEhs--------------R~~ 541 (609) T TIGR01394 478 V--FDEYEPWKPGEIETRRNGSLVSMEDGTATAYALWNLQERGRLFVSPGTEVYEGMIIGEHS--------------REN 541 (609) T ss_pred H--HHCCCCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHCCCEEECCCCCEECCEEEEECC--------------CCC T ss_conf 2--102578887687775141589926881066768738753843307886263347887238--------------866 Q ss_pred CEECCCCEEC Q ss_conf 7883662000 Q gi|254780879|r 603 GIKVDSTKVR 612 (652) Q Consensus 603 G~~VdP~~~~ 612 (652) -=-|||+|-| T Consensus 542 DL~VN~~K~K 551 (609) T TIGR01394 542 DLDVNVCKAK 551 (609) T ss_pred CCEECCCCCC T ss_conf 6602751676 No 116 >pfam08596 Lgl_C Lethal giant larvae(Lgl) like, C-terminal. The Lethal giant larvae (Lgl) tumour suppressor family is conserved from yeast to mammals. The Lgl family functions in cell polarity, at least in part, by regulating SNARE-mediated membrane delivery events at the cell surface. The N-terminal half of Lgl members contains WD40 repeats (see pfam00400), while the C-terminal half appears specific to the family. Probab=46.24 E-value=8.2 Score=17.53 Aligned_cols=142 Identities=18% Similarity=0.228 Sum_probs=61.8 Q ss_pred CCCCCCC-CCCCCCCC-CCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHH--HHH Q ss_conf 3345410-23567641-4340443464200302679672797159679996530897007999839974882002--144 Q gi|254780879|r 489 PVPFGRM-TSGFGMRY-HPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNH--QDA 564 (652) Q Consensus 489 Pv~~~ri-sS~Fg~R~-hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaH--lS~ 564 (652) ++++-.+ +|.-+-|. .|..... -|+-.|.. +...+--+|.+ -..+.|..++.=+.+|..-+|.= |.. T Consensus 224 ~i~g~vva~s~~~iRv~kp~~sK~-~hK~~~~~------~~c~~a~vv~~--~~~~~g~~LV~l~~~g~~k~ySlP~LkE 294 (393) T pfam08596 224 VIPGFVVATSVSDIRVFKPGKSKG-THKSFDYP------ILCSGASVVPT--GQRKHGIVLVALFINGSIKVYSLPSLKE 294 (393) T ss_pred EEEEEEEEECCCCEEEECCCCCCC-CCEEECCC------EECCEEEEEEE--CCCCCCEEEEEEECCCCEEEEECCCHHH T ss_conf 541499998677607972766655-41000363------02140599762--1357706999996698189983676365 Q ss_pred H-----H-----HCCCCCCEEECCCEEEEECCCCCCCCCEEEEEEEECCE----------ECCCCEECCCCCCCCCHHHH Q ss_conf 5-----4-----11889978834958998416678887426889978678----------83662000788787888999 Q gi|254780879|r 565 I-----A-----KNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVNGI----------KVDSTKVRIPERENLKGDLL 624 (652) Q Consensus 565 ~-----a-----~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vnG~----------~VdP~~~~lp~~~~l~~~~l 624 (652) | . +..+...--+-|++++++|.+-.+ .++ ++-.|+ -.||-. .+|..-....-+- T Consensus 295 i~~~~lp~~~~~~~~~~s~i~~~GDi~~~~gp~E~~---l~~--v~g~~~~~~~~~~~D~l~Np~~-~iPpRPtis~lqW 368 (393) T pfam08596 295 IKKMKLPFPIDARYLSESSILRNGDIFIRTGPTEAA---LIS--VFGSSSTGAELPPTDLLYNPNA-AIPPRPQVSSLQW 368 (393) T ss_pred HCCCCCCCCCCCCCCCCCEECCCCCEEEECCCCCEE---EEE--EECCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCC T ss_conf 401468866575533474682899989861874168---999--8647654567896010348445-6899885420012 Q ss_pred HHHHH--HHHHHHHHHHCCCCCC Q ss_conf 99999--9999999984147766 Q gi|254780879|r 625 QRFAM--EKKRINSLLNNGENPK 645 (652) Q Consensus 625 ~~F~~--~~~~id~ll~~~~~~~ 645 (652) ....+ -.+.+|.||.-..+|+ T Consensus 369 ~~GtqyvS~~dld~LigGp~RPp 391 (393) T pfam08596 369 ARGTQYCSPEDLDLLIGGPNRPP 391 (393) T ss_pred CCCCEEECHHHHHHHHCCCCCCC T ss_conf 13506509999999857999998 No 117 >PRK11160 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed Probab=46.13 E-value=15 Score=15.71 Aligned_cols=15 Identities=13% Similarity=0.242 Sum_probs=8.5 Q ss_pred CEEECCCCEEEEEEE Q ss_conf 279715967999653 Q gi|254780879|r 525 PIVAVGDGIVEKANW 539 (652) Q Consensus 525 PI~Aag~G~V~~ag~ 539 (652) -|+--.+|+|+..|. T Consensus 543 ~I~vl~~G~i~e~Gt 557 (575) T PRK11160 543 QICVMDNGQIIEQGT 557 (575) T ss_pred EEEEEECCEEEEECC T ss_conf 999998989999888 No 118 >pfam03397 Rhabdo_matrix Rhabdovirus matrix protein. Probab=45.63 E-value=8.1 Score=17.57 Aligned_cols=47 Identities=23% Similarity=0.285 Sum_probs=34.1 Q ss_pred EEEEEEEEEECCEEEEEECCCE-----EEEECCCCCCCCCCCCCCCCHHHHH Q ss_conf 6994114766674247645710-----0210023655333589798712552 Q gi|254780879|r 114 IIEVPTLIKDHNKDIIKKIPFA-----YARMTFATPYPKVKDHPKFDPLKIF 160 (652) Q Consensus 114 ~~~~~~~~~~g~r~~~~~~pf~-----~~~~~l~~~~~~~~~~p~f~p~~~~ 160 (652) .=||+++..+|+-.|--.+|=. ..+|.||..-......|.||||.-+ T Consensus 16 edrV~~~~teGtl~itG~~P~nl~eKi~~aMkLA~AIlggd~HPaFn~lv~l 67 (168) T pfam03397 16 EDRVSTILTEGTLTITGPPPGNLVEKICMAMKLARAILGGDQHPAFNPLVHL 67 (168) T ss_pred CCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHH T ss_conf 7617999855579981789974788999999999998777777440048999 No 119 >PTZ00265 multidrug resistance protein (mdr1); Provisional Probab=44.70 E-value=16 Score=15.48 Aligned_cols=35 Identities=23% Similarity=0.245 Sum_probs=21.9 Q ss_pred EEEEEHH--HHHHHHCCCCCCEEECCCEEEEECCCC--CCC Q ss_conf 4882002--144541188997883495899841667--888 Q gi|254780879|r 555 YVSSYNH--QDAIAKNIKAGTAVKQGQIIGWIGTTG--LST 591 (652) Q Consensus 555 y~T~YaH--lS~~a~gV~~G~~V~qGQvIG~vGsTG--~ST 591 (652) +.-.|.. ...+.+++. =+|+.||.||.||.|| -|| T Consensus 1172 V~F~Ypsrp~~pVLk~ls--f~I~~GqkVaiVGrSGsGKST 1210 (1467) T PTZ00265 1172 VNFRYISRPNVPIYKDLS--FSCDSKKTTAIVGETGSGKST 1210 (1467) T ss_pred EEEECCCCCCCCCCCCEE--EEECCCCEEEEECCCCCCHHH T ss_conf 999828999592018845--997799889998999983999 No 120 >PRK00044 psd phosphatidylserine decarboxylase; Reviewed Probab=44.38 E-value=7 Score=18.00 Aligned_cols=21 Identities=19% Similarity=0.460 Sum_probs=14.3 Q ss_pred HHHCCCCCCEEECCCEEEEEC Q ss_conf 541188997883495899841 Q gi|254780879|r 565 IAKNIKAGTAVKQGQIIGWIG 585 (652) Q Consensus 565 ~a~gV~~G~~V~qGQvIG~vG 585 (652) +...+++|++|+-||.||+.= T Consensus 266 ~~~~l~~g~~vr~Gq~ig~~~ 286 (291) T PRK00044 266 LAEQLEAGSPTRMGEPLAHST 286 (291) T ss_pred CCCCCCCCCEEEECHHHCCCC T ss_conf 032458999887165657940 No 121 >TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA; InterPro: IPR011917 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes .; GO: 0005524 ATP binding, 0006869 lipid transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane. Probab=43.99 E-value=15 Score=15.75 Aligned_cols=47 Identities=15% Similarity=0.044 Sum_probs=24.2 Q ss_pred ECCCCCHHHH---HHH--CCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEE Q ss_conf 4179708999---997--4999899999999854015610169988899997 Q gi|254780879|r 281 IQHNTTIFDA---MVH--AGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGV 327 (652) Q Consensus 281 VK~GDTL~~I---L~r--~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~ 327 (652) +==.||++.= -+. .+++.++|.+++.+-+-.-=.++|..|=...|+- T Consensus 446 ~LFdDTiA~NvaYg~~da~~~~~a~v~~A~~~Ayl~dfvd~lP~Gldt~vG~ 497 (603) T TIGR02203 446 VLFDDTIANNVAYGRLDAEQVDRAEVERALAAAYLQDFVDKLPLGLDTPVGE 497 (603) T ss_pred EECCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC T ss_conf 7205326776440423400178789999999864688871478885634241 No 122 >PRK06823 ornithine cyclodeaminase; Validated Probab=43.66 E-value=16 Score=15.46 Aligned_cols=14 Identities=0% Similarity=0.147 Sum_probs=5.9 Q ss_pred CCCCHHHCCCCCEE Q ss_conf 01561016998889 Q gi|254780879|r 310 NEVRVDQLTKDEIL 323 (652) Q Consensus 310 ~~~~~~~Lr~Gq~L 323 (652) ..++...|++|..+ T Consensus 205 Pv~~~~~lkpG~hi 218 (315) T PRK06823 205 PLLQAEDIQPGTHI 218 (315) T ss_pred CCCCCCCCCCCCEE T ss_conf 64165557899679 No 123 >PRK09282 pyruvate carboxylase subunit B; Validated Probab=43.36 E-value=20 Score=14.83 Aligned_cols=17 Identities=29% Similarity=0.348 Sum_probs=9.8 Q ss_pred CCCCEEECCCCEEEEEE Q ss_conf 96727971596799965 Q gi|254780879|r 522 RGTPIVAVGDGIVEKAN 538 (652) Q Consensus 522 ~GTPI~Aag~G~V~~ag 538 (652) .+++|-|.-.|.|++.- T Consensus 510 ~~~~V~APmpG~V~~V~ 526 (580) T PRK09282 510 AGGPVTAPMAGNIVKVL 526 (580) T ss_pred CCCEECCCCCCEEEEEE T ss_conf 99853279982699999 No 124 >PRK11892 pyruvate dehydrogenase subunit beta; Provisional Probab=43.34 E-value=12 Score=16.47 Aligned_cols=24 Identities=13% Similarity=0.218 Sum_probs=10.1 Q ss_pred CCCCCCCCCCCCCCCCCCCCEEEEEEE Q ss_conf 111222212331000134630699411 Q gi|254780879|r 93 LSSMQRARLSPKTKSKHPEKIIIEVPT 119 (652) Q Consensus 93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 119 (652) ++.-+.++...-.+ .+|-++++.. T Consensus 27 gd~v~~gd~~aeie---tdkatme~ea 50 (464) T PRK11892 27 GDKVKSGDVIAEIE---TDKATMEVEA 50 (464) T ss_pred CCCCCCCCEEEEEE---ECCEEEEEEE T ss_conf 97525786689975---0656689875 No 125 >PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed Probab=43.04 E-value=18 Score=15.17 Aligned_cols=35 Identities=14% Similarity=0.202 Sum_probs=18.0 Q ss_pred CCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHH Q ss_conf 7279715967999653089700799983997488200214 Q gi|254780879|r 524 TPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQD 563 (652) Q Consensus 524 TPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS 563 (652) .-|+--.+|.|+..|..-- .+..++-|...|+|+. T Consensus 551 D~Iivld~G~Ive~Gth~e-----Ll~~~g~Y~~l~~~q~ 585 (588) T PRK11174 551 DQILVMQDGKIVQQGDYAE-----LSQAQGLFATLLAHRQ 585 (588) T ss_pred CEEEEEECCEEEEECCHHH-----HHHCCCHHHHHHHHHH T ss_conf 9999998988999888999-----9849997899999987 No 126 >pfam07831 PYNP_C Pyrimidine nucleoside phosphorylase C-terminal domain. This domain is found at the C-terminal end of the large alpha/beta domain making up various pyrimidine nucleoside phosphorylases. It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside phosphorylase (PYNP) there is an added three-stranded anti-parallel beta sheet as compared to other members of the family, such as E. coli thymidine phosphorylase (TP). The domain contains an alpha/ beta hammerhead fold and residues in this domain seem to be important in formation of the homodimer. Probab=42.80 E-value=20 Score=14.77 Aligned_cols=18 Identities=33% Similarity=0.387 Sum_probs=12.7 Q ss_pred CCCCCEEECCCEEEEECC Q ss_conf 889978834958998416 Q gi|254780879|r 569 IKAGTAVKQGQIIGWIGT 586 (652) Q Consensus 569 V~~G~~V~qGQvIG~vGs 586 (652) .+.|++|++||.|..+=+ T Consensus 38 ~k~Gd~V~~g~pl~~i~~ 55 (75) T pfam07831 38 KKVGDKVKKGDPLATIYA 55 (75) T ss_pred CCCCCEECCCCEEEEEEC T ss_conf 468999669993999977 No 127 >COG4054 McrB Methyl coenzyme M reductase, beta subunit [Coenzyme metabolism] Probab=41.91 E-value=21 Score=14.68 Aligned_cols=54 Identities=22% Similarity=0.287 Sum_probs=34.0 Q ss_pred CCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEECC--CCCEEEEECCCCEEE Q ss_conf 434044346420030267967279715967999653089--700799983997488 Q gi|254780879|r 504 HPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWAGG--YGKQTLIHHGNGYVS 557 (652) Q Consensus 504 hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~G--yGn~V~I~H~~Gy~T 557 (652) +-||-|-.---||||.-..||-|==.-=---+|-|-..| .||.|+-||..|+-- T Consensus 339 NDilEyETGLPgvDfGraeGtAVGFSFFSHSIYGGGGPGiF~GNHvVTRHSkGFAi 394 (447) T COG4054 339 NDILEYETGLPGVDFGRAEGTAVGFSFFSHSIYGGGGPGIFNGNHVVTRHSKGFAI 394 (447) T ss_pred HHHHHHHCCCCCCCCCCCCCEEEEEEEEEEEEECCCCCCCCCCCEEEEECCCCCCC T ss_conf 44666623998765454343275556432100058988640486467743677544 No 128 >pfam01887 SAM_adeno_trans S-adenosyl-l-methionine hydroxide adenosyltransferase. This is a family of proteins, previously known as DUF62, found in archaebacteria and bacteria. The structure of proteins in this family is similar to that of a bacterial fluorinating enzyme. S-adenosyl-l-methionine hydroxide adenosyltransferases utilizes a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to hydroxide ion. This family used to be known as DUF62. Probab=41.71 E-value=21 Score=14.66 Aligned_cols=22 Identities=27% Similarity=0.696 Sum_probs=14.6 Q ss_pred EECCCEEEEECCCCCCCCCEEEEEEEECC Q ss_conf 83495899841667888742688997867 Q gi|254780879|r 575 VKQGQIIGWIGTTGLSTGPHLHYELIVNG 603 (652) Q Consensus 575 V~qGQvIG~vGsTG~STGPHLHfEv~vnG 603 (652) |..|+...|.||.| +.||-+|. T Consensus 220 v~~G~~~~~~~S~G-------~lEIavn~ 241 (258) T pfam01887 220 VPPGELLAYVNSSG-------FLEIAVNQ 241 (258) T ss_pred CCCCCEEEEECCCC-------CEEEEECC T ss_conf 79998899998999-------19999817 No 129 >cd06849 lipoyl_domain Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid dehydrogenase (BCDH), contain at least three different enzymes, 2-oxo acid dehydrogenase (E1), dihydrolipoyl acyltransferase (E2) and dihydrolipoamide dehydrogenase (E3) and play a key role in redox regulation. E2, the central component of the complex, catalyzes the transfer of the acyl group of CoA from E1 to E3 via reductive acetylation of a lipoyl group covalently attached to a lysine residue. Probab=41.66 E-value=20 Score=14.78 Aligned_cols=29 Identities=24% Similarity=0.325 Sum_probs=16.6 Q ss_pred EEEEHHHHHHHH--CCCCCCEEECCCEEEEE Q ss_conf 882002144541--18899788349589984 Q gi|254780879|r 556 VSSYNHQDAIAK--NIKAGTAVKQGQIIGWI 584 (652) Q Consensus 556 ~T~YaHlS~~a~--gV~~G~~V~qGQvIG~v 584 (652) ...++..+.... -+++|+.|+.||+|+++ T Consensus 44 ~~i~a~~~G~v~~i~~~~G~~v~~G~~l~~i 74 (74) T cd06849 44 VEVEAPAAGVLAKILVEEGDTVPVGQVIAVI 74 (74) T ss_pred EEEECCCCEEEEEEEECCCCEECCCCEEEEC T ss_conf 8410798999999987899998899999979 No 130 >PRK10125 predicted glycosyl transferase; Provisional Probab=41.36 E-value=10 Score=16.88 Aligned_cols=40 Identities=18% Similarity=0.239 Sum_probs=24.9 Q ss_pred CCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCC Q ss_conf 267967279715967999653089700799983997488200214454118 Q gi|254780879|r 519 AAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNI 569 (652) Q Consensus 519 aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV 569 (652) |-.+||||+|-..|=+- -+|+|.|||+-.|.--..++.++ T Consensus 326 a~acg~pvv~~~~~g~~-----------~~~~~~~g~~~~~~d~~~la~~i 365 (405) T PRK10125 326 ALSIGVPVIATHSDAAR-----------EVLQKSGGKTVSEEEVLQLAQLS 365 (405) T ss_pred HHHCCCCEEEECCCCCH-----------HHEECCCCEEECCCCHHHHHHHH T ss_conf 99749988983599973-----------65115874596688999999989 No 131 >cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae. Probab=40.34 E-value=17 Score=15.23 Aligned_cols=48 Identities=19% Similarity=0.236 Sum_probs=24.7 Q ss_pred CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHC---CCCCCEEECCCEE Q ss_conf 96799965308970079998399748820021445411---8899788349589 Q gi|254780879|r 531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKN---IKAGTAVKQGQII 581 (652) Q Consensus 531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~g---V~~G~~V~qGQvI 581 (652) .|+|... --||=+|.|.+.++-..--.|.|.++.. -.+.+-++.||.| T Consensus 5 ~G~V~~i---~~fGaFV~l~~~~~~~~GLvHiSeis~~~~~~~~~~~~~~G~~V 55 (79) T cd05684 5 KGKVTSI---MDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKV 55 (79) T ss_pred EEEEEEE---EEEEEEEEEECCCCCCEEEEEHHHCCCCCCCCCHHHHCCCCCEE T ss_conf 9999899---75339999967889806789956815755558988936799999 No 132 >COG4656 RnfC Predicted NADH:ubiquinone oxidoreductase, subunit RnfC [Energy production and conversion] Probab=40.19 E-value=14 Score=15.88 Aligned_cols=23 Identities=13% Similarity=0.094 Sum_probs=11.5 Q ss_pred EEEECCCCCHHHHHHHCCCCHHH Q ss_conf 68841797089999974999899 Q gi|254780879|r 278 LIPIQHNTTIFDAMVHAGYSNGD 300 (652) Q Consensus 278 ~v~VK~GDTL~~IL~r~Gvs~~e 300 (652) .+.|+=|..+..+|...|.-..+ T Consensus 299 nv~VrIGTP~~~lL~~~G~~~~~ 321 (529) T COG4656 299 NVWVRIGTPVSQLLNEAGGIDTK 321 (529) T ss_pred EEEEECCCCHHHHHHHCCCCCCC T ss_conf 08997789499999974897678 No 133 >TIGR01924 rsbW_low_gc anti-sigma B factor; InterPro: IPR010193 This entry describes the anti-sigma B factor also known as serine-protein kinase RsbW. Sigma B controls the general stress regulon in B subtilis and is activated by cell stresses such as stationary phase and heat shock. RsbW binds to sigma B and prevents formation of the transcription complex at the promoter . RsbV (anti-anti-sigma factor) binds to RsbW to inhibit association with sigma B, however RsbW can phosphorylate RsbV, causing disassociation of the RsbV/RsbW complex . Low ATP level or environmental stress causes the dephosphorylation of RsbV .; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0016989 sigma factor antagonist activity, 0006468 protein amino acid phosphorylation, 0045892 negative regulation of transcription DNA-dependent. Probab=39.89 E-value=15 Score=15.60 Aligned_cols=60 Identities=15% Similarity=0.305 Sum_probs=32.2 Q ss_pred CCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECCCCC-CCEEEEEEECCCCCEEEEE Q ss_conf 708999997499989999999985401561016998889999727888-6405899971688348999 Q gi|254780879|r 285 TTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQKDD-KFTIVRFSIYHKQKHLLTI 351 (652) Q Consensus 285 DTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~~~~-~~~~~r~si~~~~~~~~~v 351 (652) =||+.|+.|.|+++++|.-+==|.+... .+.. .=.+....+ ..--+++.+|.+.....+. T Consensus 25 LtlSGvasR~GytYd~IED~KIAVSEA~-TN~V------~HAYke~~nvG~~~i~F~iyEDklev~vs 85 (161) T TIGR01924 25 LTLSGVASRAGYTYDDIEDLKIAVSEAC-TNAV------KHAYKEEENVGEISIEFEIYEDKLEVIVS 85 (161) T ss_pred EEEHHHHHHCCCCHHHHHHHHHHHHHHH-CCCE------EEEECCCCCEEEEEEEEEEEEEEEEEEEE T ss_conf 4102565524878657520677665553-0331------12230898367899888788757899982 No 134 >PRK08225 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated Probab=39.72 E-value=22 Score=14.45 Aligned_cols=15 Identities=20% Similarity=0.435 Sum_probs=8.8 Q ss_pred CCCCCEEECCCEEEE Q ss_conf 889978834958998 Q gi|254780879|r 569 IKAGTAVKQGQIIGW 583 (652) Q Consensus 569 V~~G~~V~qGQvIG~ 583 (652) +++|+.|..||++.. T Consensus 54 v~~Gd~V~~G~~L~~ 68 (70) T PRK08225 54 VQEGDFVNEGDVLLE 68 (70) T ss_pred ECCCCEECCCCEEEE T ss_conf 589899899999999 No 135 >TIGR03505 FimV_core FimV N-terminal domain. This region is found at, or about 200 amino acids from, the N-terminus of FimV from Pseudomonas aeruginosa, TspA of Neisseria meningitidis, and related proteins. Disruption of FimV blocks twitching motility from type IV pili; Semmler, et al. suggest a role for this family in peptidoglycan layer remodelling required by type IV fimbrial systems. Most but not all members of this protein family have a C-terminal region recognized by TIGR03504. In between is a highly variable, often repeat-filled region rich in the negatively charged amino acids Asp and Glu. Probab=38.97 E-value=23 Score=14.37 Aligned_cols=43 Identities=16% Similarity=0.094 Sum_probs=28.3 Q ss_pred CCHHHHHHHCC----CCHHHHHHHHHHHHC----CCCHHHCCCCCEEEEEE Q ss_conf 70899999749----998999999998540----15610169988899997 Q gi|254780879|r 285 TTIFDAMVHAG----YSNGDSAKIAKALKN----EVRVDQLTKDEILRIGV 327 (652) Q Consensus 285 DTL~~IL~r~G----vs~~ei~~i~~al~~----~~~~~~Lr~Gq~L~I~~ 327 (652) |||++|+.++- ++..+++-.+...|. ..+.+.|+.|..|+++. T Consensus 1 dTLw~IA~~~~~~~~~s~~Q~M~ai~~~Np~AF~~~niN~L~~g~~L~iP~ 51 (74) T TIGR03505 1 DTLWGIAQRVRPDNSVSLYQMMLALYRANPDAFIGGNINRLKVGQILRIPS 51 (74) T ss_pred CCHHHHHHHHCCCCCCCHHHHHHHHHHHCHHHHHCCCHHHHCCCCEEECCC T ss_conf 958999998776889899999999999895977348831323799555859 No 136 >PRK10790 putative multidrug transporter membrane\ATP-binding components; Provisional Probab=38.86 E-value=20 Score=14.77 Aligned_cols=15 Identities=13% Similarity=0.155 Sum_probs=9.1 Q ss_pred CEEECCCCEEEEEEE Q ss_conf 279715967999653 Q gi|254780879|r 525 PIVAVGDGIVEKANW 539 (652) Q Consensus 525 PI~Aag~G~V~~ag~ 539 (652) -|+=-.+|.|+..|. T Consensus 543 ~I~vl~~G~ive~Gt 557 (593) T PRK10790 543 TILVLHRGQAVEQGT 557 (593) T ss_pred EEEEEECCEEEEECC T ss_conf 999998999999727 No 137 >COG0845 AcrA Membrane-fusion protein [Cell envelope biogenesis, outer membrane] Probab=38.48 E-value=23 Score=14.32 Aligned_cols=12 Identities=17% Similarity=-0.050 Sum_probs=4.2 Q ss_pred CCCEEEEECCCC Q ss_conf 495899841667 Q gi|254780879|r 577 QGQIIGWIGTTG 588 (652) Q Consensus 577 qGQvIG~vGsTG 588 (652) .|+.|---|.++ T Consensus 347 ~G~~v~v~~~~~ 358 (372) T COG0845 347 PGDRVVVEGLFL 358 (372) T ss_pred CCCEEEEECCCC T ss_conf 998999953223 No 138 >COG0213 DeoA Thymidine phosphorylase [Nucleotide transport and metabolism] Probab=37.91 E-value=24 Score=14.26 Aligned_cols=57 Identities=30% Similarity=0.337 Sum_probs=40.5 Q ss_pred CCCCCCEEECCCCEEEEE--------EEECCCCCEEE---EECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECC Q ss_conf 679672797159679996--------53089700799---98399748820021445411889978834958998416 Q gi|254780879|r 520 APRGTPIVAVGDGIVEKA--------NWAGGYGKQTL---IHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGT 586 (652) Q Consensus 520 Ap~GTPI~Aag~G~V~~a--------g~~~GyGn~V~---I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGs 586 (652) ++.=-+|+|.-+|.|.+. .+.=|.|+.+. |+|+-|.. .| .|.|++|+.|+.|..+=+ T Consensus 333 ~~~~~~v~A~~~G~v~~id~~~ig~~a~~lGAgR~~k~d~iD~~aGi~---l~-------kk~ge~Vk~Gd~l~tiya 400 (435) T COG0213 333 AKYTAEVKAQTSGYVSEIDARAIGMAAMELGAGRATKTDRIDKGAGIY---LH-------KKLGEKVKKGDPLATIYA 400 (435) T ss_pred CCEEEEEECCCCEEEEEECHHHHHHHHHHHCCCCCCCCCCCCCCCCEE---EE-------ECCCCEECCCCEEEEEEC T ss_conf 765888864676268762558999999980899788734347556669---98-------317983026974799862 No 139 >pfam09449 DUF2020 Domain of unknown function (DUF2020). Protein of unknown function found in bacteria. Probab=37.60 E-value=24 Score=14.23 Aligned_cols=24 Identities=50% Similarity=0.822 Sum_probs=10.8 Q ss_pred CEEECCCCCCCEEECCCCEEEEEEEECCC Q ss_conf 00302679672797159679996530897 Q gi|254780879|r 515 GVDWAAPRGTPIVAVGDGIVEKANWAGGY 543 (652) Q Consensus 515 GVD~aAp~GTPI~Aag~G~V~~ag~~~Gy 543 (652) =|||+||+-+-=.|. ...||.||+ T Consensus 76 vVd~aAPid~t~pa~-----eP~GWsGGr 99 (144) T pfam09449 76 VVDWAAPIDSTEPAE-----EPAGWSGGR 99 (144) T ss_pred HHCCCCCCCCCCCCC-----CCCCCCCCC T ss_conf 734457645568476-----887753653 No 140 >COG4181 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism] Probab=37.47 E-value=16 Score=15.46 Aligned_cols=11 Identities=9% Similarity=0.184 Sum_probs=5.2 Q ss_pred EEECCCCCHHH Q ss_conf 88417970899 Q gi|254780879|r 279 IPIQHNTTIFD 289 (652) Q Consensus 279 v~VK~GDTL~~ 289 (652) ..|+.|||+.- T Consensus 31 L~v~~Ge~vai 41 (228) T COG4181 31 LVVKRGETVAI 41 (228) T ss_pred EEECCCCEEEE T ss_conf 78627865888 No 141 >TIGR01711 gspJ general secretion pathway protein J; InterPro: IPR010055 This entry represents GspJ, one of two proteins highly conserved at their N-termini and described by Bacterial type II secretion system protein I/J but is easily separable phylogenetically. The other is the General secretion pathway protein I. Both GspI and GspJ are proteins of the type II secretion pathway, or main terminal branch of the general secretion pathway. This pathway carries proteins across the outer membrane. Note that proteins of type II secretion are cryptic in Escherichia coli K-12 - present but not yet demonstrated to act on any target.; GO: 0008565 protein transporter activity, 0015628 protein secretion by the type II secretion system, 0015627 type II protein secretion system complex. Probab=37.29 E-value=20 Score=14.83 Aligned_cols=16 Identities=25% Similarity=0.302 Sum_probs=7.0 Q ss_pred CCCCEEEEEEECCCCC Q ss_conf 4672368896238854 Q gi|254780879|r 442 DDSELLYIHARFGETR 457 (652) Q Consensus 442 ~~geil~A~~~~~g~~ 457 (652) ..+++..+.....++. T Consensus 106 pRs~lqrVgwrL~~~~ 121 (202) T TIGR01711 106 PRSELQRVGWRLKDEK 121 (202) T ss_pred CCCCEEEEEEEECCCE T ss_conf 7421235444514772 No 142 >KOG2525 consensus Probab=36.90 E-value=25 Score=14.15 Aligned_cols=23 Identities=9% Similarity=0.122 Sum_probs=16.1 Q ss_pred CCEEECCCCCCCEEECCCCEEEE Q ss_conf 20030267967279715967999 Q gi|254780879|r 514 TGVDWAAPRGTPIVAVGDGIVEK 536 (652) Q Consensus 514 ~GVD~aAp~GTPI~Aag~G~V~~ 536 (652) .|++|..-.++|=+...+.+... T Consensus 394 ~~~~F~~Vvf~Pni~~~~~~~~~ 416 (496) T KOG2525 394 IGTRFSSVVFMPNITSSSPVGSA 416 (496) T ss_pred CCCCCCEEEECCCCCCCCCCCCH T ss_conf 34451417852443115876664 No 143 >PRK05559 DNA topoisomerase IV subunit B; Reviewed Probab=36.78 E-value=25 Score=14.14 Aligned_cols=11 Identities=9% Similarity=0.299 Sum_probs=5.3 Q ss_pred HHHHHHHHCCC Q ss_conf 99999984147 Q gi|254780879|r 632 KRINSLLNNGE 642 (652) Q Consensus 632 ~~id~ll~~~~ 642 (652) +.++.||.+.. T Consensus 607 ~~~~~lmg~~~ 617 (633) T PRK05559 607 ELVDMLMGKKA 617 (633) T ss_pred HHHHHHHCCCC T ss_conf 99999828995 No 144 >PRK06944 sulfur carrier protein ThiS; Provisional Probab=36.64 E-value=7.6 Score=17.74 Aligned_cols=49 Identities=12% Similarity=0.188 Sum_probs=27.8 Q ss_pred EEEECCCCCHHHHHHHCCCCHHHHHHHHHHH--HCCCCHHHCCCCCEEEEE Q ss_conf 6884179708999997499989999999985--401561016998889999 Q gi|254780879|r 278 LIPIQHNTTIFDAMVHAGYSNGDSAKIAKAL--KNEVRVDQLTKDEILRIG 326 (652) Q Consensus 278 ~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al--~~~~~~~~Lr~Gq~L~I~ 326 (652) ...+..|.|+.++|..+++.+.-+.++...+ +.......|+.|+++.|. T Consensus 9 ~~~lp~g~tvadll~~l~~~~~~AVavN~~~VPRs~~~~~~L~~GD~ieiv 59 (65) T PRK06944 9 TLSLPDGATVADALAAYGARPPFAVAVNGNFVARTQHAARALAAGDRLDLV 59 (65) T ss_pred EEECCCCCCHHHHHHHCCCCCCEEEEECCEEECHHHHHHCCCCCCCEEEEE T ss_conf 642799997999998628689779998479803145333127899999999 No 145 >PRK12727 flagellar biosynthesis regulator FlhF; Provisional Probab=36.53 E-value=22 Score=14.50 Aligned_cols=25 Identities=16% Similarity=0.321 Sum_probs=14.8 Q ss_pred CHHHHHHHCCCCHHHHHHHHHHHHC Q ss_conf 0899999749998999999998540 Q gi|254780879|r 286 TIFDAMVHAGYSNGDSAKIAKALKN 310 (652) Q Consensus 286 TL~~IL~r~Gvs~~ei~~i~~al~~ 310 (652) .|..-|.+.|++..=+..++..+.. T Consensus 294 ~L~krL~~~GfS~~Lar~L~~~lP~ 318 (557) T PRK12727 294 QALELMDDYGFDAGLTRDVAMQIPA 318 (557) T ss_pred HHHHHHHHCCCCHHHHHHHHHHCCC T ss_conf 9999999766999999999974833 No 146 >PRK13657 cyclic beta-1,2-glucan ABC transporter; Provisional Probab=36.00 E-value=25 Score=14.06 Aligned_cols=52 Identities=8% Similarity=0.035 Sum_probs=25.1 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCC Q ss_conf 223342226654456777764013688417970899999749998999999998540156 Q gi|254780879|r 254 IIEENRTITSPQVLIDKIPEFADDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVR 313 (652) Q Consensus 254 ~~~en~t~~~~~~~~~~~~~~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~ 313 (652) +.=+||++.-+.. .+...+-...|++|++++- .-..|--...+.++ +.+.++ T Consensus 335 I~~~~VsF~Y~~~----~~vL~~isl~i~~Ge~vai-VG~SGsGKSTL~~L---L~gly~ 386 (585) T PRK13657 335 VEFDDVSFSYDNS----RQAVEDVSFEAKPGQTVAI-VGPTGAGKSTLINL---LHRVFD 386 (585) T ss_pred EEEEEEEEECCCC----CCCCCCCEEEECCCCEEEE-ECCCCCCHHHHHHH---HHHHCC T ss_conf 9999879867999----8753670389759988999-88989869999999---860157 No 147 >smart00566 consensus Probab=35.95 E-value=25 Score=14.11 Aligned_cols=11 Identities=64% Similarity=1.159 Sum_probs=8.2 Q ss_pred CEEEEEEEECC Q ss_conf 42688997867 Q gi|254780879|r 593 PHLHYELIVNG 603 (652) Q Consensus 593 PHLHfEv~vnG 603 (652) .+|||+|..|| T Consensus 79 ~slhy~~~~~G 89 (90) T smart00566 79 GSLHYQLLVNG 89 (90) T ss_pred CCEEEEEEEEC T ss_conf 94999999704 No 148 >PTZ00243 ABC transporter; Provisional Probab=35.88 E-value=26 Score=14.04 Aligned_cols=53 Identities=23% Similarity=0.304 Sum_probs=29.6 Q ss_pred CEEEEEH-HHHHHHHCCCCCCEEECCCEEEEECCCCC--CCCCEEE--------EEEEECCEECCC Q ss_conf 7488200-21445411889978834958998416678--8874268--------899786788366 Q gi|254780879|r 554 GYVSSYN-HQDAIAKNIKAGTAVKQGQIIGWIGTTGL--STGPHLH--------YELIVNGIKVDS 608 (652) Q Consensus 554 Gy~T~Ya-HlS~~a~gV~~G~~V~qGQvIG~vGsTG~--STGPHLH--------fEv~vnG~~VdP 608 (652) ++...|. ++.-..++|. =+|+.||.||-||-||- ||=-.+= =.|.++|.-+.= T Consensus 1313 nVs~rYr~~lp~VLk~Is--f~I~pGEKVGIVGRTGSGKSSLi~aLfRl~e~~~G~I~IDGvDIs~ 1376 (1560) T PTZ00243 1313 GVQMRYREGLPLVLRGVS--FRIAPREKVGIVGRTGSGKSTLLLTFMRMVEVCGGEIRVNGREIGA 1376 (1560) T ss_pred EEEEECCCCCCCCCCCEE--EEECCCCEEEEECCCCCHHHHHHHHHHCCCCCCCCEEEECCEEHHH T ss_conf 889972899987105746--9988999999987987439999999970327788989997998202 No 149 >PRK01734 consensus Probab=35.49 E-value=14 Score=15.94 Aligned_cols=34 Identities=6% Similarity=-0.015 Sum_probs=18.5 Q ss_pred HHHHHHCCCCHHHHHHH-H---HHHHCCCCHHHCCCCCE Q ss_conf 99999749998999999-9---98540156101699888 Q gi|254780879|r 288 FDAMVHAGYSNGDSAKI-A---KALKNEVRVDQLTKDEI 322 (652) Q Consensus 288 ~~IL~r~Gvs~~ei~~i-~---~al~~~~~~~~Lr~Gq~ 322 (652) ..-.+.|+++-+|+..= . .+|+..+ .++|++|-+ T Consensus 49 ~~fik~y~inl~Ea~~~~~~~Y~sfn~FF-tR~LKp~aR 86 (294) T PRK01734 49 KAFAKKYNVDMSEAQKENFSDYASFNEFF-IRPLKENAR 86 (294) T ss_pred HHHHHHHCCCHHHHCCCCHHHCCCHHHHE-ECCCCCCCC T ss_conf 99999979897897469812168789928-111666665 No 150 >COG1217 TypA Predicted membrane GTPase involved in stress response [Signal transduction mechanisms] Probab=35.26 E-value=26 Score=13.98 Aligned_cols=57 Identities=30% Similarity=0.376 Sum_probs=41.1 Q ss_pred CCCCCEEEEECCCCEEEEEHHHHHHHHC---CCCCCEEECCCEEEEECCCCCCCCCEEEEEEEECCEECCCCEE Q ss_conf 8970079998399748820021445411---8899788349589984166788874268899786788366200 Q gi|254780879|r 541 GGYGKQTLIHHGNGYVSSYNHQDAIAKN---IKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVNGIKVDSTKV 611 (652) Q Consensus 541 ~GyGn~V~I~H~~Gy~T~YaHlS~~a~g---V~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vnG~~VdP~~~ 611 (652) ++--|-|.|...+|-.|.|+-+.-=-+| |.+|++|=+|++||.-- |-|---|||+|- T Consensus 480 ~~R~nGvLiS~~~G~a~~yal~~lqdRG~~Fi~pG~~vYeGmiiG~hs--------------R~nDL~VN~~k~ 539 (603) T COG1217 480 GGRHNGVLISNETGKAVAYALFNLQDRGKLFIEPGTKVYEGMIIGEHS--------------RDNDLTVNVLKG 539 (603) T ss_pred CCCCCCEEEECCCCCCHHHHHHHHHHCCCEEECCCCCEEEEEEEEEEC--------------CCCCCEECCCCC T ss_conf 555451599768984347655358753756645997265016985306--------------756713424234 No 151 >pfam11545 HemeBinding_Shp Cell surface heme-binding protein Shp. Shp is part of a complex which functions in heme uptake in Streptococcus pyogenes. During which, Shp transfers its heme to HtsA which is a component of an ABC transporter. The heme binding region of Shp contains an immunoglobulin-like beta-sandwich fold and has a unique heme-iron coordination with the axial ligands being two methionine residues from the same Shp molecule. Surrounding the heme pocket, there is a negative surface which may serve as a docking interface for heme transfer. Probab=34.87 E-value=26 Score=13.94 Aligned_cols=97 Identities=18% Similarity=0.236 Sum_probs=58.2 Q ss_pred CCCCCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEE-ECCCCEEEEEHHHHHHHHCCCCCCEEECC- Q ss_conf 6414340443464200302679672797159679996530897007999-83997488200214454118899788349- Q gi|254780879|r 501 MRYHPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLI-HHGNGYVSSYNHQDAIAKNIKAGTAVKQG- 578 (652) Q Consensus 501 ~R~hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I-~H~~Gy~T~YaHlS~~a~gV~~G~~V~qG- 578 (652) ..+||+.|.. .-+-|++-+|.|.|-|+-+=|..+ +++. +-+.-|.|.=.||-.+.++++ -||..+ T Consensus 13 sY~hPvTG~i--------ED~Gg~~~~aiGqgMVe~~V~s~~---llE~td~Gk~YlTvr~~L~d~~sn~~--f~VQ~~g 79 (151) T pfam11545 13 NYRHPVSGQI--------EDSGGEHSFDIGQGMVEGTVYSDG---MLEVTDAGKIYLTFRMSLADYSGNYQ--FWVQPGG 79 (151) T ss_pred CCCCCCCCEE--------ECCCCCCCCCHHHHHHHHEECCCE---EEEECCCCCEEEEEEEEEHHCCCCCE--EEEEECC T ss_conf 5458775357--------348987562111123121441541---69981799789999976201267835--9998789 Q ss_pred ------CEEEEECCCCCCCCCEEEEEEEECC--------EECCCCE Q ss_conf ------5899841667888742688997867--------8836620 Q gi|254780879|r 579 ------QIIGWIGTTGLSTGPHLHYELIVNG--------IKVDSTK 610 (652) Q Consensus 579 ------QvIG~vGsTG~STGPHLHfEv~vnG--------~~VdP~~ 610 (652) .-+...|+.-...|--.||.|-++. -+|.||- T Consensus 80 dg~f~~va~t~T~~g~d~ngtt~D~ri~vps~n~vvr~smYVePMG 125 (151) T pfam11545 80 TGSFQAVAYNITQKGTDTNGTTLDIAISLPTVNSVVRGSMYVEPMG 125 (151) T ss_pred CCCEEEEEEEEECCCCCCCCCEEEEEEECCCCCCEEEEEEEECCCC T ss_conf 8960350067620130279965779996288881898999982489 No 152 >cd03245 ABCC_bacteriocin_exporters ABC-type bacteriocin exporters. Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two glycine residues in positions -1 and -2. A dedicated ATP-binding cassette (ABC) transporter is responsible for the proteolytic cleavage of the leader peptides and subsequent translocation of the bacteriocins across the cytoplasmic membrane. Probab=34.66 E-value=27 Score=13.91 Aligned_cols=24 Identities=8% Similarity=0.124 Sum_probs=9.1 Q ss_pred EEEECCCCCHHHHHHHCCCCHHHHH Q ss_conf 6884179708999997499989999 Q gi|254780879|r 278 LIPIQHNTTIFDAMVHAGYSNGDSA 302 (652) Q Consensus 278 ~v~VK~GDTL~~IL~r~Gvs~~ei~ 302 (652) ...|++|+.+. |.-..|--...+. T Consensus 24 sl~i~~G~~v~-ivG~sGsGKSTLl 47 (220) T cd03245 24 SLTIRAGEKVA-IIGRVGSGKSTLL 47 (220) T ss_pred EEEECCCCEEE-EECCCCCHHHHHH T ss_conf 99987999999-9999998599999 No 153 >COG1156 NtpB Archaeal/vacuolar-type H+-ATPase subunit B [Energy production and conversion] Probab=34.22 E-value=27 Score=13.87 Aligned_cols=29 Identities=14% Similarity=-0.003 Sum_probs=19.1 Q ss_pred CCCCCCCCCCCHHHHHHHHCCCCCCCCCC Q ss_conf 34444445565033443202333222456 Q gi|254780879|r 195 ITRIQLDHTAQDEEIKNAIMNQFFLLHNK 223 (652) Q Consensus 195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 223 (652) ..+.-..+.+...+...+++.+..+..+. T Consensus 148 KlPIFSgSGlphN~LaaqIarQA~v~~~~ 176 (463) T COG1156 148 KLPIFSGSGLPHNELAAQIARQATVDGEE 176 (463) T ss_pred CCCCCCCCCCCHHHHHHHHHHHCCCCCCC T ss_conf 46601279984379999999753667875 No 154 >COG0508 AceF Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component, and related enzymes [Energy production and conversion] Probab=33.76 E-value=26 Score=14.02 Aligned_cols=14 Identities=21% Similarity=0.389 Sum_probs=7.2 Q ss_pred CCCCCHHHHHHHHH Q ss_conf 78788899999999 Q gi|254780879|r 616 RENLKGDLLQRFAM 629 (652) Q Consensus 616 ~~~l~~~~l~~F~~ 629 (652) .|.++|.+-+.|.. T Consensus 376 HRviDGa~a~~Fl~ 389 (404) T COG0508 376 HRVIDGAEAARFLV 389 (404) T ss_pred CCCCCCHHHHHHHH T ss_conf 63327387889999 No 155 >cd03249 ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1. In fact, the yeast MDL1 (multidrug resistance-like protein 1) and MDL2 (multidrug resistance-like protein 2) transporters are also included in this CD. MDL1 is an ATP-dependent permease that acts as a high-copy suppressor of ATM1 and is thought to have a role in resistance to oxidative stress. Interestingly, subfamily B is more closely related to the carboxyl-terminal component of subfamily C than the two halves of ABCC molecules are with one another. Probab=33.61 E-value=28 Score=13.80 Aligned_cols=14 Identities=21% Similarity=0.299 Sum_probs=6.6 Q ss_pred CEEECCCCEEEEEE Q ss_conf 27971596799965 Q gi|254780879|r 525 PIVAVGDGIVEKAN 538 (652) Q Consensus 525 PI~Aag~G~V~~ag 538 (652) -|+--.+|.|+..| T Consensus 206 ~Iivl~~G~Ive~G 219 (238) T cd03249 206 LIAVLQNGQVVEQG 219 (238) T ss_pred EEEEEECCEEEEEC T ss_conf 99999899999988 No 156 >COG1726 NqrA Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrA [Energy production and conversion] Probab=33.51 E-value=19 Score=14.92 Aligned_cols=17 Identities=18% Similarity=0.290 Sum_probs=8.4 Q ss_pred HHHHCCCCCCCCCCCCC Q ss_conf 87626884100486200 Q gi|254780879|r 62 LTALDGHQKIAIPAKLS 78 (652) Q Consensus 62 ~~aldg~~~~a~p~~~~ 78 (652) +.||+|+.-..+++.+. T Consensus 28 ~Vallg~ey~gmrp~mk 44 (447) T COG1726 28 EVALLGEEYVGMRPSMK 44 (447) T ss_pred EEEECCCCCCCCCCCCE T ss_conf 79871651468887415 No 157 >TIGR00062 L27 ribosomal protein L27; InterPro: IPR001684 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . L27 is a protein from the large (50S) subunit; it is essential for ribosome function, but its exact role is unclear. It belongs to a family of ribosomal proteins, examples of which are found in bacteria, chloroplasts of plants and red algae and the mitochondria of fungi (e.g. MRP7 from yeast mitochondria). The schematic relationship between these groups of proteins is shown below. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome. Probab=33.36 E-value=28 Score=13.77 Aligned_cols=30 Identities=17% Similarity=0.325 Sum_probs=25.8 Q ss_pred CCCCCCEEECCCCCCCEEECCCCEEEEEEE Q ss_conf 346420030267967279715967999653 Q gi|254780879|r 510 SRMHTGVDWAAPRGTPIVAVGDGIVEKANW 539 (652) Q Consensus 510 ~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~ 539 (652) .++|.|-..+.-.-.-|+|..||+|.|.-. T Consensus 43 Tk~~~G~NVg~G~D~tlFA~~~G~V~f~~~ 72 (83) T TIGR00062 43 TKFYPGENVGLGKDDTLFALSDGVVKFEKK 72 (83) T ss_pred CEEECCCEEECCCCCEEEECCCCEEEEEEC T ss_conf 652178500037885366515885876345 No 158 >cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export. They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. Probab=33.20 E-value=28 Score=13.75 Aligned_cols=29 Identities=14% Similarity=0.189 Sum_probs=14.5 Q ss_pred CEEEEEECCCCCHHHHHHHCCCCHHHHHHH Q ss_conf 013688417970899999749998999999 Q gi|254780879|r 275 ADDLIPIQHNTTIFDAMVHAGYSNGDSAKI 304 (652) Q Consensus 275 ~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i 304 (652) ..-...|++|+.+ .|.-+.|.-.....++ T Consensus 19 ~~isl~i~~Ge~i-~ivG~sGsGKSTLl~l 47 (171) T cd03228 19 KDVSLTIKPGEKV-AIVGPSGSGKSTLLKL 47 (171) T ss_pred ECEEEEECCCCEE-EEECCCCCHHHHHHHH T ss_conf 7718998599899-9999999839999999 No 159 >TIGR01729 taurine_ABC_bnd taurine ABC transporter, periplasmic binding protein; InterPro: IPR010068 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry identifies a cluster of ABC transporter periplasmic substrate binding proteins, apparently specific for taurine. Transport systems for taurine (NH2-CH2-CH2-SO3H), sulphonates, and sulphate esters import sulphur when sulphate levels are low. The most closely related proteins outside this family are putative aliphatic sulphonate binding proteins.. Probab=32.69 E-value=9.7 Score=17.01 Aligned_cols=13 Identities=31% Similarity=0.519 Sum_probs=6.5 Q ss_pred CCHHHHHHHHHHH Q ss_conf 9989999999973 Q gi|254780879|r 399 MNSNLVKLIMRTL 411 (652) Q Consensus 399 ip~~ii~~lv~i~ 411 (652) .++.++.+|++.. T Consensus 198 knPe~v~aF~Kv~ 210 (304) T TIGR01729 198 KNPEVVKAFVKVL 210 (304) T ss_pred HCHHHHHHHHHHH T ss_conf 0707899999889 No 160 >PRK06549 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated Probab=32.62 E-value=29 Score=13.69 Aligned_cols=17 Identities=29% Similarity=0.421 Sum_probs=12.5 Q ss_pred CCCCCEEECCCEEEEEC Q ss_conf 88997883495899841 Q gi|254780879|r 569 IKAGTAVKQGQIIGWIG 585 (652) Q Consensus 569 V~~G~~V~qGQvIG~vG 585 (652) +++|+.|..||++-.+| T Consensus 116 v~~G~~V~~g~~L~~ig 132 (132) T PRK06549 116 VGPGQVVNPGDGLITIG 132 (132) T ss_pred ECCCCEECCCCEEEEEC T ss_conf 47989989999899949 No 161 >PRK10584 putative ABC transporter ATP-binding protein YbbA; Provisional Probab=32.47 E-value=29 Score=13.67 Aligned_cols=12 Identities=8% Similarity=0.191 Sum_probs=5.2 Q ss_pred CCEEECCCCEEE Q ss_conf 727971596799 Q gi|254780879|r 524 TPIVAVGDGIVE 535 (652) Q Consensus 524 TPI~Aag~G~V~ 535 (652) .-|+.--||.|+ T Consensus 214 drvi~l~~G~Iv 225 (228) T PRK10584 214 DRRLRLVNGQLQ 225 (228) T ss_pred CCEEEEECCEEE T ss_conf 979999899999 No 162 >COG4615 PvdE ABC-type siderophore export system, fused ATPase and permease components [Secondary metabolites biosynthesis, transport, and catabolism / Inorganic ion transport and metabolism] Probab=32.38 E-value=20 Score=14.79 Aligned_cols=25 Identities=16% Similarity=0.142 Sum_probs=12.8 Q ss_pred EEEECCCCCHHHHHHHCCCCHHHHHH Q ss_conf 68841797089999974999899999 Q gi|254780879|r 278 LIPIQHNTTIFDAMVHAGYSNGDSAK 303 (652) Q Consensus 278 ~v~VK~GDTL~~IL~r~Gvs~~ei~~ 303 (652) ...+|+||-+.-| -.+|-....... T Consensus 343 Nl~ikrGelvFli-G~NGsGKST~~~ 367 (546) T COG4615 343 NLTIKRGELVFLI-GGNGSGKSTLAM 367 (546) T ss_pred EEEEECCCEEEEE-CCCCCCHHHHHH T ss_conf 3687337389998-889963889999 No 163 >cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology. Probab=32.11 E-value=27 Score=13.92 Aligned_cols=22 Identities=14% Similarity=0.225 Sum_probs=7.8 Q ss_pred ECCCCCHHHHHHHCCCCHHHHHH Q ss_conf 41797089999974999899999 Q gi|254780879|r 281 IQHNTTIFDAMVHAGYSNGDSAK 303 (652) Q Consensus 281 VK~GDTL~~IL~r~Gvs~~ei~~ 303 (652) |++|+.+ .|+-.+|.-.....+ T Consensus 22 v~~GEiv-~ilGpNGaGKSTllk 43 (177) T cd03222 22 VKEGEVI-GIVGPNGTGKTTAVK 43 (177) T ss_pred CCCCCEE-EEECCCCCCHHHHHH T ss_conf 5899899-998999999999999 No 164 >TIGR01474 ubiA_proteo 4-hydroxybenzoate polyprenyl transferase; InterPro: IPR006370 These sequences are a family of integral membrane proteins that condense para-hydroxybenzoate with any of several polyprenyldiphosphates. Heterologous expression studies suggest that for, many but not all members, the activity seen (e.g. octaprenyltransferase in Escherichia coli) reflects available host isoprenyl pools rather than enzyme specificity. A fairly deep split by both clustering (UPGMA) and phylogenetics (NJ tree) separates this group (mostly Proteobacterial and mitochondrial), with several characterised members, from another group (mostly archaeal and Gram-positive bacterial) lacking characterised members IPR006371 from INTERPRO .; GO: 0004659 prenyltransferase activity, 0009058 biosynthetic process, 0016021 integral to membrane. Probab=31.57 E-value=6.9 Score=18.07 Aligned_cols=17 Identities=24% Similarity=0.112 Sum_probs=10.0 Q ss_pred CCCCCCCCCCCCCEEEHH Q ss_conf 476544578854113189 Q gi|254780879|r 24 GNNDAKIFLDNRRKVSLR 41 (652) Q Consensus 24 ~~~~~~~~~~~rr~vs~r 41 (652) |++.+.++++ =++||.| T Consensus 74 VeRTk~RPLa-sG~vs~~ 90 (291) T TIGR01474 74 VERTKSRPLA-SGAVSVR 90 (291) T ss_pred CCCCCCCCCC-CCCCHHH T ss_conf 4000037874-6631189 No 165 >TIGR01381 E1_like_apg7 E1-like protein-activating enzyme Gsa7p/Apg7p; InterPro: IPR006285 This is a family of eukaryotic proteins found in animals, plants, and yeasts that includes Apg7p (YHR171W) from Saccharomyces cerevisiae and GSA7 from Pichia pastoris. Members are about 650 to 700 residues in length and include a central domain of about 150 residues shared with the ThiF/MoeB/HesA family of proteins. A low level of similarity to ubiquitin-activating enzyme E1 is described in a paper on peroxisome autophagy mediated by GSA7, and is the basis of the name ubiquitin activating enzyme E1-like protein. Members of the family appear to be involved in protein lipidation events analogous to ubiquitination and required for membrane fusion events during autophagy. . Probab=31.44 E-value=28 Score=13.81 Aligned_cols=119 Identities=18% Similarity=0.191 Sum_probs=58.6 Q ss_pred CCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCC---------- Q ss_conf 1246723688962388542013455766554443355661000001123334541023567641434044---------- Q gi|254780879|r 440 ASDDSELLYIHARFGETRTRFYRFLNPVDGSVEYFNENGKSSRPFLLRTPVPFGRMTSGFGMRYHPILGY---------- 509 (652) Q Consensus 440 ~~~~geil~A~~~~~g~~~~~yrf~~~~~~~~~yyd~~G~S~~k~llr~Pv~~~risS~Fg~R~hPilg~---------- 509 (652) ++++|++-|-.... -..|.|++--.+...-...-.+++++-|.-.-..+-++.= -|--|||.-. T Consensus 377 FvDngkVs~sNPVR----QsL~nFeDcl~gG~~KAetA~kalk~IFP~i~~~g~~l~v--PMpGHpi~~~~~~~~~~D~~ 450 (689) T TIGR01381 377 FVDNGKVSYSNPVR----QSLYNFEDCLEGGEGKAETAAKALKRIFPAIEASGYRLEV--PMPGHPIDEKDVDELLEDIK 450 (689) T ss_pred EEECCEEEECCCCC----CCCCCHHHHHCCCCHHHHHHHHHHHHHCHHHHCCCEEEEE--CCCCCCCCCCCHHHHHHHHH T ss_conf 86457454027746----8764336451378623899999998625002015317861--68888887221266899999 Q ss_pred -----CCCCCCE----EECCCCCCC-EEECCCCEEEEEEEECCCCCEEEEECCCC-EEEEEHHHHHH Q ss_conf -----3464200----302679672-79715967999653089700799983997-48820021445 Q gi|254780879|r 510 -----SRMHTGV----DWAAPRGTP-IVAVGDGIVEKANWAGGYGKQTLIHHGNG-YVSSYNHQDAI 565 (652) Q Consensus 510 -----~r~H~GV----D~aAp~GTP-I~Aag~G~V~~ag~~~GyGn~V~I~H~~G-y~T~YaHlS~~ 565 (652) .+-|.-| |=.=.+==| |.++---+ |-+.-.=|+--|++||||+| ..+.---|+.- T Consensus 451 rL~~Lik~HDvVFLl~DsRE~RWLPtvLc~~~~K-IaI~aAlGFDsY~v~RHG~gs~~~~~~d~~~~ 516 (689) T TIGR01381 451 RLEELIKEHDVVFLLLDSREARWLPTVLCARFDK-IAISAALGFDSYLVMRHGAGSRSEEVSDVEES 516 (689) T ss_pred HHHHHHHHCCEEEEECCCCHHHHHHHHHHHCCCC-EEEEEEECCCEEEEEECCCCCCCCCHHHHHHC T ss_conf 9999865005355301365002237899753794-48887423360577762788865302335442 No 166 >PTZ00085 40S ribosomal protein S28; Provisional Probab=31.26 E-value=15 Score=15.59 Aligned_cols=53 Identities=19% Similarity=0.285 Sum_probs=27.2 Q ss_pred CCEEEEECCCCCCCCCEEEEEEEECCEECCCCEECCCCCCCCCHHHHHHHHHHHH Q ss_conf 9589984166788874268899786788366200078878788899999999999 Q gi|254780879|r 578 GQIIGWIGTTGLSTGPHLHYELIVNGIKVDSTKVRIPERENLKGDLLQRFAMEKK 632 (652) Q Consensus 578 GQvIG~vGsTG~STGPHLHfEv~vnG~~VdP~~~~lp~~~~l~~~~l~~F~~~~~ 632 (652) =+|+|..||+|-.|. +.-||+-++..-+-.-++.-.|..-.|+.|.=.+.||+ T Consensus 10 ~~vlGRTG~~G~~tQ--Vrv~~l~~~~~~gR~i~RNVkGPVr~GDIL~LlEtERE 62 (67) T PTZ00085 10 EKVLGRTGSRGGVTQ--VRVQFMGESELEGRTLIRNVKGPVREGDILALLETERE 62 (67) T ss_pred EEEECCCCCCCCEEE--EEEEEECCCCCCCCEEEEECCCCCCCCCEEEEEHHHHH T ss_conf 999525557686799--99999218886686988804277335649875214446 No 167 >PTZ00144 dihydrolipoamide succinyltransferase; Provisional Probab=30.82 E-value=31 Score=13.49 Aligned_cols=23 Identities=9% Similarity=0.059 Sum_probs=15.0 Q ss_pred CCEECCCCCCCCCHHHHHHHHHHH Q ss_conf 620007887878889999999999 Q gi|254780879|r 608 STKVRIPERENLKGDLLQRFAMEK 631 (652) Q Consensus 608 P~~~~lp~~~~l~~~~l~~F~~~~ 631 (652) ++.+ --..|.++|..-++|.... T Consensus 395 ~lsL-s~DHRviDGa~aArFl~~l 417 (430) T PTZ00144 395 NLAL-TYDHRLIDGRDAVQFLNAI 417 (430) T ss_pred EEEE-EEECCCCCHHHHHHHHHHH T ss_conf 9889-7233030639999999999 No 168 >COG1912 Uncharacterized conserved protein [Function unknown] Probab=30.42 E-value=31 Score=13.44 Aligned_cols=46 Identities=22% Similarity=0.356 Sum_probs=32.8 Q ss_pred EEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCCCCEEEEEEEEC-CEECCCCEECC Q ss_conf 200214454118899788349589984166788874268899786-78836620007 Q gi|254780879|r 558 SYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVN-GIKVDSTKVRI 613 (652) Q Consensus 558 ~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vn-G~~VdP~~~~l 613 (652) .|.+.-+| ++.=-.|..||.+.|+|| |-|.||-+| |..-+-+.++. T Consensus 213 ~~~~k~~~---v~tfg~v~~Ge~l~~~nS-------~g~lEiaVn~Gsaa~~l~v~~ 259 (268) T COG1912 213 VYGNKIPF---VKTFGDVDEGELLALINS-------LGNLEIAVNMGSAAEKLGVKE 259 (268) T ss_pred EEEEEEEE---EEEECCCCCCCEEEEECC-------CCCEEEEEECCCHHHHHCCCC T ss_conf 86217656---731134788976898658-------770899985488889719887 No 169 >COG0444 DppD ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism] Probab=29.86 E-value=32 Score=13.38 Aligned_cols=14 Identities=7% Similarity=0.147 Sum_probs=8.8 Q ss_pred CCCCCEEEEEEEEE Q ss_conf 14454068875321 Q gi|254780879|r 421 LKPTDFLETFFSVN 434 (652) Q Consensus 421 ir~GD~f~Vlye~~ 434 (652) .+--|+.-|+|... T Consensus 218 a~~aDrv~VMYaG~ 231 (316) T COG0444 218 AEIADRVAVMYAGR 231 (316) T ss_pred HHHCCEEEEEECCE T ss_conf 97456689987758 No 170 >pfam08710 nsp9 nsp9 replicase. nsp9 is a single-stranded RNA-binding viral protein likely to be involved in RNA synthesis. Its structure comprises of a single beta barrel. Probab=29.40 E-value=32 Score=13.33 Aligned_cols=33 Identities=24% Similarity=0.417 Sum_probs=21.9 Q ss_pred ECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCCC Q ss_conf 839974882002144541188997883495899841667 Q gi|254780879|r 550 HHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTG 588 (652) Q Consensus 550 ~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG 588 (652) +-++|-+-.|..- ||--...++|.|+|+.|+|= T Consensus 76 ~~~~g~~vkYLYF------VKnln~L~RG~VlG~I~aTV 108 (111) T pfam08710 76 DTPKGPEVKYLYF------VKNLNNLRRGAVLGYIGATV 108 (111) T ss_pred ECCCCCEEEEEEE------ECCCCHHHCCEEEEEEEEEE T ss_conf 8699978999998------61643010003887633799 No 171 >TIGR01348 PDHac_trf_long pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase; InterPro: IPR006256 This group of sequences are a subset of pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase specifically close by both phylogenetic and percent identity (UPGMA) trees. Members contain two or three copies of the lipoyl-binding domain. Escherichia coli AceF is included in this set while mitochondrial and some other bacterial forms are excluded. dihydrolipoyllysine-residue acetyltransferase E2 component of pyruvate dehydrogenase complex; GO: 0004742 dihydrolipoyllysine-residue acetyltransferase activity, 0006096 glycolysis, 0045254 pyruvate dehydrogenase complex. Probab=29.25 E-value=31 Score=13.41 Aligned_cols=31 Identities=6% Similarity=-0.021 Sum_probs=20.4 Q ss_pred EEEEEECCEEEEEECCCEEEEECCCCCCCCCCCCCC Q ss_conf 114766674247645710021002365533358979 Q gi|254780879|r 118 PTLIKDHNKDIIKKIPFAYARMTFATPYPKVKDHPK 153 (652) Q Consensus 118 ~~~~~~g~r~~~~~~pf~~~~~~l~~~~~~~~~~p~ 153 (652) ++-.++|| +.+--++-|.|-.....++.-|. T Consensus 56 ~ikvkVGD-----t~~~G~~i~~l~~~~g~a~aaPa 86 (655) T TIGR01348 56 EIKVKVGD-----TLKEGDVIALLEVSAGSASAAPA 86 (655) T ss_pred EEEEEECC-----CCCCCCEEEEECCCCCCCCCCCC T ss_conf 89754466-----54778789997166532135776 No 172 >TIGR01437 selA_rel pyridoxal phosphate-dependent enzyme, putative; InterPro: IPR006337 Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). PLP is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination , , . PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors . Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy . PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the epsilon-amino group of an active site lysine residue on the enzyme. The alpha-amino group of the substrate displaces the lysine epsilon-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalyzed reactions, enzymatic and non-enzymatic . This entry represents a group of proteins that are related to a number of pyridoxal phosphate-dependent enzymes, and in particular to selenocysteine synthase (SelA), which converts Ser to selenocysteine on its tRNA. While resembling SelA, this protein is found only in species that have a better candidate SelA or else lack the other genes (selB, selC, and selD) required for selenocysteine incorporation. . Probab=29.13 E-value=16 Score=15.54 Aligned_cols=22 Identities=41% Similarity=0.382 Sum_probs=13.5 Q ss_pred HHHHHHHHHHH-HHHHCCCCCCC Q ss_conf 99999999999-87626884100 Q gi|254780879|r 51 ITSGVIIGGSL-LTALDGHQKIA 72 (652) Q Consensus 51 ~~~~~l~g~a~-~~aldg~~~~a 72 (652) ||+|+==|.|+ .|||=+....+ T Consensus 66 Its~AsAGia~~vAali~~g~~a 88 (391) T TIGR01437 66 ITSGASAGIALAVAALISKGTRA 88 (391) T ss_pred HHHHHHHHHHHHHHHHHCCCCCC T ss_conf 89878889999999975167632 No 173 >cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR). DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus. Probab=29.10 E-value=33 Score=13.29 Aligned_cols=47 Identities=11% Similarity=-0.044 Sum_probs=19.5 Q ss_pred CCCCCCCCCCCCCC-CCCCCEEEEEECCCCCHHHHHHHCCCCHHHHHHH Q ss_conf 34222665445677-7764013688417970899999749998999999 Q gi|254780879|r 257 ENRTITSPQVLIDK-IPEFADDLIPIQHNTTIFDAMVHAGYSNGDSAKI 304 (652) Q Consensus 257 en~t~~~~~~~~~~-~~~~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i 304 (652) +|++..-+...... .+--..-...|++|+.+ .|+-..|--.....++ T Consensus 7 ~nls~~y~~~~~~~~k~iL~~vs~~v~~Gei~-~ilGpnGaGKSTLl~~ 54 (194) T cd03213 7 RNLTVTVKSSPSKSGKQLLKNVSGKAKPGELT-AIMGPSGAGKSTLLNA 54 (194) T ss_pred EEEEEEECCCCCCCCCEEEECCEEEEECCEEE-EEECCCCCHHHHHHHH T ss_conf 98999978999889998788838899088199-9998999519999999 No 174 >cd00421 intradiol_dioxygenase Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. This family contains catechol 1,2-dioxygenases and protocatechuate 3,4-dioxygenases which are mononuclear non-heme iron enzymes that catalyze the oxygenation of catecholates to aliphatic acids via the cleavage of aromatic rings. The members are intradiol-cleaving enzymes which break the catechol C1-C2 bond and utilize Fe3+, as opposed to the extradiol-cleaving enzymes which break the C2-C3 or C1-C6 bond and utilize Fe2+ and Mn+. Catechol 1,2-dioxygenases are mostly homodimers with one catalytic ferric ion per monomer. Protocatechuate 3,4-dioxygenases form more diverse oligomers. Probab=28.83 E-value=33 Score=13.26 Aligned_cols=13 Identities=31% Similarity=0.897 Sum_probs=11.2 Q ss_pred CCEEEEEEEECCE Q ss_conf 7426889978678 Q gi|254780879|r 592 GPHLHYELIVNGI 604 (652) Q Consensus 592 GPHLHfEv~vnG~ 604 (652) -||+||.|..+|. T Consensus 83 ~~HIH~~v~~~g~ 95 (146) T cd00421 83 PPHIHFKVFAPGY 95 (146) T ss_pred CCEEEEEEECCCC T ss_conf 8759999981996 No 175 >cd03251 ABCC_MsbA MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. Probab=28.81 E-value=33 Score=13.26 Aligned_cols=11 Identities=36% Similarity=0.610 Sum_probs=3.6 Q ss_pred EEECCCCEEEE Q ss_conf 79715967999 Q gi|254780879|r 526 IVAVGDGIVEK 536 (652) Q Consensus 526 I~Aag~G~V~~ 536 (652) |+--.+|+|+. T Consensus 206 Iivl~~G~ive 216 (234) T cd03251 206 IVVLEDGKIVE 216 (234) T ss_pred EEEEECCEEEE T ss_conf 99998999999 No 176 >KOG0215 consensus Probab=28.74 E-value=33 Score=13.25 Aligned_cols=101 Identities=21% Similarity=0.258 Sum_probs=57.7 Q ss_pred EECCCCCEEEEECCCCEEEEEHHH--------------------------HHHHHCCCCCCEEECCCEEEEE---CCCCC Q ss_conf 308970079998399748820021--------------------------4454118899788349589984---16678 Q gi|254780879|r 539 WAGGYGKQTLIHHGNGYVSSYNHQ--------------------------DAIAKNIKAGTAVKQGQIIGWI---GTTGL 589 (652) Q Consensus 539 ~~~GyGn~V~I~H~~Gy~T~YaHl--------------------------S~~a~gV~~G~~V~qGQvIG~v---GsTG~ 589 (652) -+.|||++.+-+|.-...-.|++. +.+ +.+|.+|+-||++=-- -.||. T Consensus 783 lDRGfGRC~Vyk~~~~~~kkY~N~T~Drimgp~~d~~t~kpi~kh~vLd~DGl---~~pG~~V~~~qi~iNK~mP~vt~~ 859 (1153) T KOG0215 783 IDRGFGRCEVYKKTTTTLKKYANGTFDRIMGPQLDPNTRKPIWKHQVLDDDGL---ATPGERVQPGQIYINKQMPTVTGT 859 (1153) T ss_pred HCCCCCEEEEEEEEEEEEEECCCCCHHHHCCCCCCCCCCCCCHHHCCCCCCCC---CCCCCEECCCCEEEECCCCCCCCC T ss_conf 11575248998600666640578751332365447876783022115375557---787537326857982567875566 Q ss_pred CCCCEEEEEEEECCEECCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 88742688997867883662000788787888999999999999999984147766 Q gi|254780879|r 590 STGPHLHYELIVNGIKVDSTKVRIPERENLKGDLLQRFAMEKKRINSLLNNGENPK 645 (652) Q Consensus 590 STGPHLHfEv~vnG~~VdP~~~~lp~~~~l~~~~l~~F~~~~~~id~ll~~~~~~~ 645 (652) ..|-+|-- .++-.--|+..|-|...-++.-++..=..+---|.-||..-++|+ T Consensus 860 -~~~~~~~~--~~~Yk~~pitykgpepsyidkVmls~n~~dq~LIK~llRQTRrPE 912 (1153) T KOG0215 860 -SLPGLSAS--QVQYKAVPITYKGPEPSYIDRVMLTSNDEDQFLIKVLLRQTRRPE 912 (1153) T ss_pred -CCCCCCCC--CCCCCCCCCEECCCCCCHHHEEEEECCCCCCHHHHHHHHHCCCCC T ss_conf -57777765--533321641433898232122676227432189999986436864 No 177 >KOG1885 consensus Probab=28.63 E-value=33 Score=13.24 Aligned_cols=34 Identities=24% Similarity=0.410 Sum_probs=19.0 Q ss_pred EEEEEEECCEEC-CCCEECCCCCCCCCHHHHHHHHHHHHH Q ss_conf 688997867883-662000788787888999999999999 Q gi|254780879|r 595 LHYELIVNGIKV-DSTKVRIPERENLKGDLLQRFAMEKKR 633 (652) Q Consensus 595 LHfEv~vnG~~V-dP~~~~lp~~~~l~~~~l~~F~~~~~~ 633 (652) =.||+.++|+-+ |-.+ .| .=+-.+++.|+.|... T Consensus 465 eRFElFi~~kEicNAYt-El----NdP~~Qr~rFe~Q~~~ 499 (560) T KOG1885 465 ERFELFIAGKEICNAYT-EL----NDPVDQRQRFEQQARD 499 (560) T ss_pred HHHHHHHCCHHHHHHHH-HH----CCHHHHHHHHHHHHHH T ss_conf 67787541088754666-60----6889999999999877 No 178 >TIGR02408 ectoine_ThpD ectoine hydroxylase; InterPro: IPR012774 Both ectoine and hydroxyectoine are compatible solvents that serve as protectants against osmotic and thermal stresses. A number of genomes synthesize ectoine. This enzyme allows conversion of ectoine to hydroxyectoine, which may be more effective for some purposes, and is found in a subset of ectoine-producing organisms.; GO: 0016725 oxidoreductase activity acting on CH or CH2 groups. Probab=28.44 E-value=17 Score=15.25 Aligned_cols=10 Identities=10% Similarity=0.159 Sum_probs=5.1 Q ss_pred HHHCCCCHHH Q ss_conf 8871999899 Q gi|254780879|r 394 TSFNGMNSNL 403 (652) Q Consensus 394 a~~~gip~~i 403 (652) ++..|+|... T Consensus 190 ~Q~~GvPd~~ 199 (278) T TIGR02408 190 KQEVGVPDEV 199 (278) T ss_pred CCCCCCCCHH T ss_conf 0678898778 No 179 >cd03288 ABCC_SUR2 The SUR domain 2. The sulfonylurea receptor SUR is an ATP binding cassette (ABC) protein of the ABCC/MRP family. Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel. Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism. It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity. Probab=28.01 E-value=34 Score=13.17 Aligned_cols=44 Identities=9% Similarity=-0.001 Sum_probs=18.5 Q ss_pred CCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHCCCCHHHHHH Q ss_conf 334222665445677776401368841797089999974999899999 Q gi|254780879|r 256 EENRTITSPQVLIDKIPEFADDLIPIQHNTTIFDAMVHAGYSNGDSAK 303 (652) Q Consensus 256 ~en~t~~~~~~~~~~~~~~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~ 303 (652) =+|+++.-+.... +....-...|++|+.+. |.-+.|--...+.+ T Consensus 22 ~~nvsf~Y~~~~~---~vL~~inl~I~~Ge~va-IvG~sGsGKSTL~~ 65 (257) T cd03288 22 IHDLCVRYENNLK---PVLKHVKAYIKPGQKVG-ICGRTGSGKSSLSL 65 (257) T ss_pred EEEEEEEECCCCC---CCEECEEEEECCCCEEE-EECCCCCCHHHHHH T ss_conf 9989999398995---73105389987999999-99999981999999 No 180 >cd04100 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Included in this group are archeal and archeal-like A Probab=27.97 E-value=34 Score=13.16 Aligned_cols=70 Identities=17% Similarity=0.271 Sum_probs=39.3 Q ss_pred EEEEEEE---CCCCC--EEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCCC---CEEEEEEEECC Q ss_conf 9996530---89700--79998399748820021445411889978834958998416678887---42688997867 Q gi|254780879|r 534 VEKANWA---GGYGK--QTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLSTG---PHLHYELIVNG 603 (652) Q Consensus 534 V~~ag~~---~GyGn--~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~STG---PHLHfEv~vnG 603 (652) |.-+||- ...|+ ++.||.+.|..-.+.+.+......+.=...+.|.+|.-.|.--.+.. +.-.|||.+.. T Consensus 2 V~v~Gwv~~~R~~g~~~Fi~lrD~~g~iQvv~~~~~~~~~~~~~~~l~~es~I~v~G~v~~~~~~~~~~g~~Ei~~~~ 79 (85) T cd04100 2 VTLAGWVHSRRDHGGLIFIDLRDGSGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVKRPEGNLATGEIELQAEE 79 (85) T ss_pred EEEEEEEEEEECCCCEEEEEEECCCCEEEEEECCCCCHHHHHHHHCCCCCCEEEEEEEEEECCCCCCCCCCEEEEEEE T ss_conf 999998790432898899585038950899991775857887763589888999999999688777899889999939 No 181 >PRK00624 glycine cleavage system protein H; Provisional Probab=27.94 E-value=34 Score=13.16 Aligned_cols=19 Identities=16% Similarity=0.421 Sum_probs=8.1 Q ss_pred CCCCEEECCCEEEEECCCC Q ss_conf 8997883495899841667 Q gi|254780879|r 570 KAGTAVKQGQIIGWIGTTG 588 (652) Q Consensus 570 ~~G~~V~qGQvIG~vGsTG 588 (652) +.|++|++|+.+|.+-|.. T Consensus 40 ~~G~~v~~g~~~~~iEs~K 58 (113) T PRK00624 40 SVGSFCKEGEVLVILESSK 58 (113) T ss_pred CCCCEEECCCEEEEEEECC T ss_conf 9999884798599999652 No 182 >PRK10789 putative multidrug transporter membrane\ATP-binding components; Provisional Probab=27.57 E-value=35 Score=13.11 Aligned_cols=16 Identities=13% Similarity=0.302 Sum_probs=10.3 Q ss_pred CCEEECCCCEEEEEEE Q ss_conf 7279715967999653 Q gi|254780879|r 524 TPIVAVGDGIVEKANW 539 (652) Q Consensus 524 TPI~Aag~G~V~~ag~ 539 (652) .-|+=-.+|.|+..|. T Consensus 517 D~I~vl~~G~ive~Gt 532 (569) T PRK10789 517 SEIIVMQHGHIAQRGN 532 (569) T ss_pred CEEEEEECCEEEEECC T ss_conf 9899998988999727 No 183 >PRK12999 pyruvate carboxylase; Reviewed Probab=27.45 E-value=35 Score=13.10 Aligned_cols=16 Identities=38% Similarity=0.501 Sum_probs=9.2 Q ss_pred CCCCCEEECCCEEEEE Q ss_conf 8899788349589984 Q gi|254780879|r 569 IKAGTAVKQGQIIGWI 584 (652) Q Consensus 569 V~~G~~V~qGQvIG~v 584 (652) |++|++|++||.+--+ T Consensus 1093 Vk~GD~VkkGd~Llvl 1108 (1147) T PRK12999 1093 VKEGDEVKAGDPLLVI 1108 (1147) T ss_pred ECCCCEECCCCEEEEE T ss_conf 6899987899989998 No 184 >PRK09473 oppD oligopeptide transporter ATP-binding component; Provisional Probab=27.41 E-value=35 Score=13.09 Aligned_cols=24 Identities=8% Similarity=0.300 Sum_probs=12.6 Q ss_pred ECCCCCHHHHHHH-CCCCHHHHHHH Q ss_conf 4179708999997-49998999999 Q gi|254780879|r 281 IQHNTTIFDAMVH-AGYSNGDSAKI 304 (652) Q Consensus 281 VK~GDTL~~IL~r-~Gvs~~ei~~i 304 (652) .+-|+.+...+.. .+++..++.+- T Consensus 114 ~~i~~~l~e~l~~~~~~~~~~~~~~ 138 (330) T PRK09473 114 MRVGEQLMEVLMLHKGMSKAEAFEE 138 (330) T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHH T ss_conf 0456655578988538998999999 No 185 >PTZ00109 DNA gyrase subunit b; Provisional Probab=27.39 E-value=35 Score=13.09 Aligned_cols=19 Identities=16% Similarity=0.263 Sum_probs=13.7 Q ss_pred CCCHHHHHHHHHHHCCCCH Q ss_conf 9998999999997301110 Q gi|254780879|r 398 GMNSNLVKLIMRTLASSVN 416 (652) Q Consensus 398 gip~~ii~~lv~i~a~dVD 416 (652) -+...-|..|+..++..|. T Consensus 624 il~N~EI~~LItAlG~Gig 642 (941) T PTZ00109 624 IFENSELKSLITAIGLNVN 642 (941) T ss_pred HHCCHHHHHHHHHHCCCCC T ss_conf 4404999999998586867 No 186 >cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain. They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substra Probab=27.02 E-value=35 Score=13.05 Aligned_cols=30 Identities=10% Similarity=0.195 Sum_probs=14.8 Q ss_pred CCEEEEEECCCCCHHHHHHHCCCCHHHHHHH Q ss_conf 4013688417970899999749998999999 Q gi|254780879|r 274 FADDLIPIQHNTTIFDAMVHAGYSNGDSAKI 304 (652) Q Consensus 274 ~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i 304 (652) ...-...|++|+.+. |.-..|--.....++ T Consensus 18 L~~i~l~i~~G~~va-IvG~sGsGKSTLl~l 47 (173) T cd03246 18 LRNVSFSIEPGESLA-IIGPSGSGKSTLARL 47 (173) T ss_pred EECEEEEECCCCEEE-EECCCCCHHHHHHHH T ss_conf 547699985999999-999999809999999 No 187 >PRK11022 dppD dipeptide transporter ATP-binding subunit; Provisional Probab=26.70 E-value=36 Score=13.01 Aligned_cols=13 Identities=0% Similarity=0.118 Sum_probs=8.8 Q ss_pred CCCCEEEEEEEEE Q ss_conf 4454068875321 Q gi|254780879|r 422 KPTDFLETFFSVN 434 (652) Q Consensus 422 r~GD~f~Vlye~~ 434 (652) +-.|++-|+|... T Consensus 219 ~~aDri~VMy~G~ 231 (327) T PRK11022 219 EAAHKIIVMYAGQ 231 (327) T ss_pred HHCCEEEEEECCE T ss_conf 8699899998988 No 188 >pfam04203 Sortase Sortase family. The founder member of this family is S.aureus sortase, a transpeptidase that attaches surface proteins by the threonine of an LPXTG motif to the cell wall. Probab=26.62 E-value=36 Score=13.00 Aligned_cols=28 Identities=21% Similarity=0.389 Sum_probs=12.2 Q ss_pred CCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEE Q ss_conf 700799983997488200214454118899788 Q gi|254780879|r 543 YGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAV 575 (652) Q Consensus 543 yGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V 575 (652) -||.|+-=|. ++-+.+++|.. +++|+.| T Consensus 38 ~gn~viaGH~-~~~~~F~~L~~----l~~Gd~i 65 (122) T pfam04203 38 GGNTVIAGHR-GGGTMFSRLDK----LKKGDKI 65 (122) T ss_pred CCCEEEEEEE-CCCCHHHHHHC----CCCCCEE T ss_conf 8729999873-89921335652----8899999 No 189 >pfam04017 DUF366 Domain of unknown function (DUF366). Archaeal domain of unknown function. Probab=26.50 E-value=24 Score=14.27 Aligned_cols=13 Identities=15% Similarity=0.120 Sum_probs=5.7 Q ss_pred CHHHCCCCCEEEE Q ss_conf 6101699888999 Q gi|254780879|r 313 RVDQLTKDEILRI 325 (652) Q Consensus 313 ~~~~Lr~Gq~L~I 325 (652) ...-.+.|+-|-+ T Consensus 99 g~~~~r~GDDlyv 111 (183) T pfam04017 99 GVKLTRDGDDLYV 111 (183) T ss_pred CCCCEECCCEEEE T ss_conf 9860655781687 No 190 >TIGR00030 S21p ribosomal protein S21; InterPro: IPR001911 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryote ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA . The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S21 contains 55-70 amino acid residues, and has only been found in eubacteria to date, though it has been reported that plant chloroplasts and mammalian mitochondria contain ribosomal subunit protein S21. Experimental evidence has revealed that S21 is well exposed on the surface of the Escherichia coli ribosome , and is one of the 'split proteins': these are a discrete group that are selectively removed from 30S subunits under low salt conditions and are required for the formation of activated 30S reconstitution intermediate (RI*) particles.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome. Probab=26.28 E-value=36 Score=12.96 Aligned_cols=18 Identities=11% Similarity=0.157 Sum_probs=15.5 Q ss_pred EEEECCCCCHHHHHHHCC Q ss_conf 688417970899999749 Q gi|254780879|r 278 LIPIQHNTTIFDAMVHAG 295 (652) Q Consensus 278 ~v~VK~GDTL~~IL~r~G 295 (652) .|.|+.||+|..+|++.. T Consensus 2 ~V~V~eges~d~ALr~FK 19 (58) T TIGR00030 2 TVKVKEGESIDSALRRFK 19 (58) T ss_pred EEEECCCCCHHHHHHHHH T ss_conf 025115887889999985 No 191 >cd02577 PSTD1 PSTD1: Pseudouridine synthase, a subgroup of the TruD family. This group consists of several hypothetical archeal pseudouridine synthases assigned to the TruD family of psuedouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). The TruD family is comprised of proteins related to Escherichia coli TruD. Probab=26.13 E-value=37 Score=12.94 Aligned_cols=12 Identities=17% Similarity=0.039 Sum_probs=5.7 Q ss_pred HHHCCCCHHHHH Q ss_conf 997499989999 Q gi|254780879|r 291 MVHAGYSNGDSA 302 (652) Q Consensus 291 L~r~Gvs~~ei~ 302 (652) .+..|++..++. T Consensus 46 Ar~lgv~~~~ig 57 (319) T cd02577 46 AKALGISRKRIG 57 (319) T ss_pred HHHHCCCHHHEE T ss_conf 998299877751 No 192 >COG1038 PycA Pyruvate carboxylase [Energy production and conversion] Probab=26.11 E-value=31 Score=13.50 Aligned_cols=23 Identities=30% Similarity=0.567 Sum_probs=15.3 Q ss_pred CCCCCEEECCCEEEEECCCCCCC Q ss_conf 88997883495899841667888 Q gi|254780879|r 569 IKAGTAVKQGQIIGWIGTTGLST 591 (652) Q Consensus 569 V~~G~~V~qGQvIG~vGsTG~ST 591 (652) |++|++|++||++.-.-.--.-| T Consensus 1095 V~~G~~Vk~Gd~l~~ieAMKMEt 1117 (1149) T COG1038 1095 VKKGDKVKKGDVLAVIEAMKMET 1117 (1149) T ss_pred ECCCCCCCCCCEEEEEHHHHHCE T ss_conf 74587304798653302232222 No 193 >PRK07440 hypothetical protein; Provisional Probab=26.06 E-value=16 Score=15.47 Aligned_cols=48 Identities=17% Similarity=0.067 Sum_probs=30.6 Q ss_pred EEECCCCCHHHHHHHCCCCHHHHHHHHH---HHHCCCCHHHCCCCCEEEEE Q ss_conf 8841797089999974999899999999---85401561016998889999 Q gi|254780879|r 279 IPIQHNTTIFDAMVHAGYSNGDSAKIAK---ALKNEVRVDQLTKDEILRIG 326 (652) Q Consensus 279 v~VK~GDTL~~IL~r~Gvs~~ei~~i~~---al~~~~~~~~Lr~Gq~L~I~ 326 (652) ..+..+-||.++|...++.+.-++-..+ ..+..++...|+.|+++.|. T Consensus 14 ~~~~~~~ti~~LL~~l~~~~~~vaVE~N~~Iv~r~~~~~~~l~~gD~iEIv 64 (70) T PRK07440 14 RTCSPGTTLPDLLQQLGFNPRLVAVEYNGEILHRQFWEQTQVQPGDRLEIV 64 (70) T ss_pred EECCCCCCHHHHHHHCCCCCCEEEEEECCEEECHHHCCCEECCCCCEEEEE T ss_conf 785999989999987699987699996886708677071067999999999 No 194 >cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis. The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism. Probab=26.00 E-value=37 Score=12.92 Aligned_cols=29 Identities=7% Similarity=0.150 Sum_probs=12.9 Q ss_pred CEEEEEECCCCCHHHHHHHCCCCHHHHHHH Q ss_conf 013688417970899999749998999999 Q gi|254780879|r 275 ADDLIPIQHNTTIFDAMVHAGYSNGDSAKI 304 (652) Q Consensus 275 ~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i 304 (652) ..-...|++|+.+. |+-..|--.....++ T Consensus 19 ~~i~l~i~~Ge~~a-ivG~sGsGKSTLl~~ 47 (178) T cd03247 19 KNLSLELKQGEKIA-LLGRSGSGKSTLLQL 47 (178) T ss_pred ECEEEEECCCCEEE-EECCCCCHHHHHHHH T ss_conf 25589986999999-999998759999999 No 195 >cd00257 Fascin Fascin-like domain; members include actin-bundling/crosslinking proteins facsin, histoactophilin and singed; identified in sea urchin, Drosophila, Xenopus, rodents, and humans; The fascin-like domain adopts a beta-trefoil topology and contains an internal threefold repeat; the fascin subgroup contains four copies of the domain; Structurally similar to fibroblast growth factor (FGF) Probab=25.99 E-value=37 Score=12.92 Aligned_cols=51 Identities=20% Similarity=0.160 Sum_probs=30.3 Q ss_pred EEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHH Q ss_conf 030267967279715967999653089700799983997488200214454 Q gi|254780879|r 516 VDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIA 566 (652) Q Consensus 516 VD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a 566 (652) +-+.+.-|--+.+..+|.|.-.+-.+.-..+.++.|++|-.+.-++.-+|. T Consensus 46 ~~lrs~~Gkyl~~~~~g~i~~~~~~~~~~~F~~e~~~~g~valka~nG~Yl 96 (119) T cd00257 46 YALRSHDGKYLSADSDGGVQLEGHPNADCRFTLEFHGDGKWALRAENGRYL 96 (119) T ss_pred EEEEECCCCEEEECCCCCEEEECCCCCCCEEEEEEECCCEEEEECCCCCEE T ss_conf 999956899999858998886057899976999991798699984899899 No 196 >pfam06898 YqfD Putative stage IV sporulation protein YqfD. This family consists of several putative bacterial stage IV sporulation (SpoIV) proteins. YqfD of Bacillus subtilis is known to be essential for efficient sporulation although its exact function is unknown. Probab=25.80 E-value=37 Score=12.90 Aligned_cols=10 Identities=20% Similarity=0.514 Sum_probs=3.3 Q ss_pred EEEEEEECCC Q ss_conf 3688962388 Q gi|254780879|r 446 LLYIHARFGE 455 (652) Q Consensus 446 il~A~~~~~g 455 (652) +.++.....| T Consensus 158 i~Wv~v~i~G 167 (383) T pfam06898 158 IMWIGVRVRG 167 (383) T ss_pred EEEEEEEEEE T ss_conf 2999999983 No 197 >COG1566 EmrA Multidrug resistance efflux pump [Defense mechanisms] Probab=25.73 E-value=37 Score=12.89 Aligned_cols=21 Identities=19% Similarity=0.289 Sum_probs=10.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9989899999999999999987 Q gi|254780879|r 42 WLSTTFFAGITSGVIIGGSLLT 63 (652) Q Consensus 42 w~~~t~ltg~~~~~l~g~a~~~ 63 (652) ++.-++++.+++. +.|.-+|. T Consensus 16 ~~~~~~~~~~~a~-~~~~~~~~ 36 (352) T COG1566 16 KLPLTLLVVLAAV-LYGGLIWL 36 (352) T ss_pred HHHHHHHHHHHHH-HHHHHHHH T ss_conf 8899999999999-99999999 No 198 >COG0050 TufB GTPases - translation elongation factors [Translation, ribosomal structure and biogenesis] Probab=25.48 E-value=33 Score=13.24 Aligned_cols=30 Identities=10% Similarity=0.148 Sum_probs=14.4 Q ss_pred HHHHHHHHHHHHCCCCHHHCCCCCEEEEEE Q ss_conf 899999999854015610169988899997 Q gi|254780879|r 298 NGDSAKIAKALKNEVRVDQLTKDEILRIGV 327 (652) Q Consensus 298 ~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~ 327 (652) .+.|.++..++..+.....=...+.+.+++ T Consensus 186 ~~~i~eLm~avd~yip~Per~~dkPflmpv 215 (394) T COG0050 186 EAKIEELMDAVDSYIPTPERDIDKPFLMPV 215 (394) T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCC T ss_conf 789999999998548999865566520101 No 199 >pfam07126 DUF1379 Protein of unknown function (DUF1379). This family consists of several hypothetical bacterial proteins of around 180 residues in length. The function of this family is unknown. Probab=25.47 E-value=38 Score=12.86 Aligned_cols=51 Identities=12% Similarity=0.139 Sum_probs=23.1 Q ss_pred CEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEE Q ss_conf 67999653089700799983997488200214454118899788349589984 Q gi|254780879|r 532 GIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWI 584 (652) Q Consensus 532 G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~v 584 (652) |.|+.-.-.+..|.+++|+++..-.+--.=-..+. +..-..-+|||+|=-+ T Consensus 90 g~~v~L~~~~~~~~flVvE~g~~asLCll~~~~~~--L~~~K~l~~~~~IKVM 140 (154) T pfam07126 90 GDLVQLKSGGETGLFLVVENGEQASLCLLLSEEFQ--LSGSKTLVQFDVIKVM 140 (154) T ss_pred CCEEEECCCCCEEEEEEEECCCCEEEEEECCCCEE--ECCCCEEECCCEEEEE T ss_conf 88899813895689999946996778887356424--0887416268738998 No 200 >COG5526 Lysozyme family protein [General function prediction only] Probab=25.42 E-value=33 Score=13.26 Aligned_cols=21 Identities=33% Similarity=0.330 Sum_probs=9.9 Q ss_pred HHHCCCCHHHHHCCCCCEEEE Q ss_conf 973011101210144540688 Q gi|254780879|r 409 RTLASSVNLQEHLKPTDFLET 429 (652) Q Consensus 409 ~i~a~dVDFqr~ir~GD~f~V 429 (652) .......||..-+..||.+.. T Consensus 65 H~~E~SlnF~thLhNGdpL~a 85 (191) T COG5526 65 HYRESSLNFGTHLHNGDPLGA 85 (191) T ss_pred HHHHCCCCCCCCCCCCCCCCC T ss_conf 431123543432468984566 No 201 >PRK05644 gyrB DNA gyrase subunit B; Validated Probab=25.34 E-value=38 Score=12.84 Aligned_cols=16 Identities=13% Similarity=0.358 Sum_probs=6.9 Q ss_pred CHHHHHHHHHHHCCCC Q ss_conf 9899999999730111 Q gi|254780879|r 400 NSNLVKLIMRTLASSV 415 (652) Q Consensus 400 p~~ii~~lv~i~a~dV 415 (652) ...-|..|+.+++.++ T Consensus 469 ~N~EI~~li~alG~g~ 484 (725) T PRK05644 469 SSEEIGTLITALGTGI 484 (725) T ss_pred CCHHHHHHHHHHCCCC T ss_conf 1879999999967788 No 202 >TIGR00955 3a01204 Pigment precourser permease; InterPro: IPR005284 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This family includes different parts of a membrane-spanning permease system necessary for the transport of pigment precursor into pigment cells responsible for eye color. White protein dimerises with brown protein for the transport of guanine and with scarlet protein for the transport of tryptophan.; GO: 0006810 transport. Probab=25.31 E-value=38 Score=12.84 Aligned_cols=58 Identities=12% Similarity=0.135 Sum_probs=35.0 Q ss_pred CCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECCCCCCC-----EEE----EEEECCCCCEEEEEEECCCC Q ss_conf 9998999999998540156101699888999972788864-----058----99971688348999842788 Q gi|254780879|r 295 GYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQKDDKF-----TIV----RFSIYHKQKHLLTIALNDNN 357 (652) Q Consensus 295 Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~~~~~~-----~~~----r~si~~~~~~~~~va~~d~g 357 (652) |+|.-.+..+++.|+++. +.|..+.+.+.++.... ++. --.+|.++..++.-=.++-| T Consensus 205 GLDSfmA~~Vv~~L~~LA-----~~G~tiI~tIHQPSs~lF~lFd~i~lla~Grvvy~G~p~~a~~FF~~~G 271 (671) T TIGR00955 205 GLDSFMAYSVVQVLKGLA-----QKGKTIICTIHQPSSELFELFDKIILLAEGRVVYLGSPDQAVPFFSELG 271 (671) T ss_pred HHHHHHHHHHHHHHHHHH-----CCCCEEEEEEECCCHHHHHHHCCEEEEECCEEEEECCCHHHHHHHHHCC T ss_conf 345999999999999985-----0897999983056188985117167752772798278103689898448 No 203 >cd03812 GT1_CapH_like This family is most closely related to the GT1 family of glycosyltransferases. capH in Staphylococcus aureus has been shown to be required for the biosynthesis of the type 1 capsular polysaccharide (CP1). Probab=25.29 E-value=38 Score=12.84 Aligned_cols=39 Identities=15% Similarity=0.085 Sum_probs=25.0 Q ss_pred ECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHH Q ss_conf 02679672797159679996530897007999839974882002144541 Q gi|254780879|r 518 WAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAK 567 (652) Q Consensus 518 ~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~ 567 (652) =|...|+||+|+..| |+-++|..+.||.....--..+|. T Consensus 285 EAma~G~PVVasd~g-----------g~~~ii~~~~~~l~~~~~~~~~a~ 323 (358) T cd03812 285 EAQASGLPCILSDTI-----------TKEVDLTDLVKFLSLDESPEIWAE 323 (358) T ss_pred HHHHHCCCEEEECCC-----------CCCEEEECCCCEEECCCCHHHHHH T ss_conf 999949989996599-----------974697299557968999999999 No 204 >PRK12835 3-ketosteroid-delta-1-dehydrogenase; Reviewed Probab=25.22 E-value=38 Score=12.83 Aligned_cols=25 Identities=4% Similarity=-0.059 Sum_probs=17.0 Q ss_pred CHHHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 1025666887199989999999973 Q gi|254780879|r 387 YDGIWRATSFNGMNSNLVKLIMRTL 411 (652) Q Consensus 387 ~~SLy~aa~~~gip~~ii~~lv~i~ 411 (652) .+||-+.|.+.|++.....+-+.-| T Consensus 429 adTleELA~~~gvd~~~L~~TV~rY 453 (584) T PRK12835 429 AHTWDELAAKIGVPAENLRATAERF 453 (584) T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHH T ss_conf 3999999988298989999999999 No 205 >PRK11176 lipid transporter ATP-binding/permease protein; Provisional Probab=25.22 E-value=30 Score=13.57 Aligned_cols=46 Identities=20% Similarity=0.169 Sum_probs=20.7 Q ss_pred CCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHCCCCHHHHHHH Q ss_conf 23342226654456777764013688417970899999749998999999 Q gi|254780879|r 255 IEENRTITSPQVLIDKIPEFADDLIPIQHNTTIFDAMVHAGYSNGDSAKI 304 (652) Q Consensus 255 ~~en~t~~~~~~~~~~~~~~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i 304 (652) .=+||++.-+.... +....-...+++|++++- .-+.|-....+.++ T Consensus 342 ~~~nVsF~Y~~~~~---~vL~~isl~I~~G~~vai-VG~SGsGKSTL~~L 387 (581) T PRK11176 342 EFRNVTFTYPGKEV---PALRNINFKIPAGKTVAL-VGRSGSGKSTIANL 387 (581) T ss_pred EEEEEEEECCCCCC---CCCCCCCCCCCCCCEEEC-CCCCCCCHHHHHHH T ss_conf 99985784489986---201066335799944312-28999867899999 No 206 >PRK07843 3-ketosteroid-delta-1-dehydrogenase; Reviewed Probab=25.15 E-value=38 Score=12.82 Aligned_cols=34 Identities=6% Similarity=0.121 Sum_probs=21.1 Q ss_pred CCHHHHHHHHHCCCCHHHHHHHHHHH------CCCCHHHH Q ss_conf 11025666887199989999999973------01110121 Q gi|254780879|r 386 IYDGIWRATSFNGMNSNLVKLIMRTL------ASSVNLQE 419 (652) Q Consensus 386 I~~SLy~aa~~~gip~~ii~~lv~i~------a~dVDFqr 419 (652) -.+||-+.|.+.|+|.....+-+.-| +.|-||.| T Consensus 418 kAdTleeLA~~~gi~~~~L~~Tv~~yN~~~~~G~D~dFgr 457 (560) T PRK07843 418 KADTLAELAGKIGLPADALTATVQRFNGFARSGVDEDFHR 457 (560) T ss_pred ECCCHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCC T ss_conf 4488999999969499999999999998885299855577 No 207 >PRK03481 consensus Probab=25.01 E-value=38 Score=12.80 Aligned_cols=36 Identities=14% Similarity=0.203 Sum_probs=23.1 Q ss_pred CCCEEEEEHHH-HHHHHCCCCCCEEECCCEEEEECCC Q ss_conf 99748820021-4454118899788349589984166 Q gi|254780879|r 552 GNGYVSSYNHQ-DAIAKNIKAGTAVKQGQIIGWIGTT 587 (652) Q Consensus 552 ~~Gy~T~YaHl-S~~a~gV~~G~~V~qGQvIG~vGsT 587 (652) |......+.-- =.+...+++|++|+-||-+|..-.| T Consensus 253 GSTVIlLF~~~~~~~~~~l~~g~~vrmGe~la~~~~~ 289 (322) T PRK03481 253 GSTVINLFAPGKVNLAEQLNSLSVTRIGQPLAESTET 289 (322) T ss_pred CCEEEEEECCCCCCCCCCCCCCCEEECCHHHHHCCCC T ss_conf 8889999458853546345899746647665411212 No 208 >PRK05704 dihydrolipoamide succinyltransferase; Validated Probab=24.99 E-value=38 Score=12.80 Aligned_cols=23 Identities=9% Similarity=0.050 Sum_probs=15.6 Q ss_pred CCEECCCCCCCCCHHHHHHHHHHH Q ss_conf 620007887878889999999999 Q gi|254780879|r 608 STKVRIPERENLKGDLLQRFAMEK 631 (652) Q Consensus 608 P~~~~lp~~~~l~~~~l~~F~~~~ 631 (652) ++.. --..|.++|..-++|.... T Consensus 370 ~lsl-s~DHRvidGa~aa~Fl~~l 392 (406) T PRK05704 370 YLAL-SYDHRIIDGKEAVGFLVTI 392 (406) T ss_pred EEEE-EEECHHCCCHHHHHHHHHH T ss_conf 9879-7452030739999999999 No 209 >cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1). NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters. Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate. Probab=24.91 E-value=39 Score=12.79 Aligned_cols=44 Identities=14% Similarity=0.101 Sum_probs=19.1 Q ss_pred CCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHCCCCHHHHHHH Q ss_conf 342226654456777764013688417970899999749998999999 Q gi|254780879|r 257 ENRTITSPQVLIDKIPEFADDLIPIQHNTTIFDAMVHAGYSNGDSAKI 304 (652) Q Consensus 257 en~t~~~~~~~~~~~~~~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i 304 (652) +|+++.-.... .+....-...|++|+.+. |.-..|--...+.++ T Consensus 10 ~nvsf~Y~~~~---~~iL~~isl~i~~Ge~v~-ivG~sGsGKSTLl~l 53 (207) T cd03369 10 ENLSVRYAPDL---PPVLKNVSFKVKAGEKIG-IVGRTGAGKSTLILA 53 (207) T ss_pred EEEEEECCCCC---CCCEEEEEEEECCCCEEE-EECCCCCCHHHHHHH T ss_conf 98899929899---672402588986999999-999999879999999 No 210 >PRK04350 thymidine phosphorylase; Provisional Probab=24.73 E-value=39 Score=12.76 Aligned_cols=53 Identities=26% Similarity=0.270 Sum_probs=36.1 Q ss_pred CCCCCCEEECCCCEEEEEEE--------ECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECC Q ss_conf 67967279715967999653--------08970079998399748820021445411889978834958998416 Q gi|254780879|r 520 APRGTPIVAVGDGIVEKANW--------AGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGT 586 (652) Q Consensus 520 Ap~GTPI~Aag~G~V~~ag~--------~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGs 586 (652) ++.=.+|.|..+|.|....- .-|.|+ +|+-|.. -.+|.|++|++||.+..+=+ T Consensus 414 a~~~~~v~A~~~G~V~~ID~~~ig~~a~~aGAp~----D~~aGI~----------l~~KvGd~V~kGdpL~tIhA 474 (502) T PRK04350 414 GDHTYDVLAPRDGYVTAIDNRRLARIARLAGAPK----DKGAGID----------LHKKIGDKVKKGDPLYTIYA 474 (502) T ss_pred CCEEEEEECCCCEEEEEECHHHHHHHHHHCCCCC----CCCCCEE----------EEECCCCEECCCCEEEEEEC T ss_conf 8857999769984999851499999999719998----8704479----------96048799679984999966 No 211 >cd04949 GT1_gtfA_like This family is most closely related to the GT1 family of glycosyltransferases and is named after gtfA in Streptococcus gordonii, where it plays a role in the O-linked glycosylation of GspB, a cell surface glycoprotein involved in platelet binding. In general glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltra Probab=24.61 E-value=23 Score=14.35 Aligned_cols=42 Identities=31% Similarity=0.582 Sum_probs=29.3 Q ss_pred ECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECC-CCEEEEEHHHHHHHHCC Q ss_conf 02679672797159679996530897007999839-97488200214454118 Q gi|254780879|r 518 WAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHG-NGYVSSYNHQDAIAKNI 569 (652) Q Consensus 518 ~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~-~Gy~T~YaHlS~~a~gV 569 (652) =|...|+||+|. +-.||..-.|+|+ |||..-++--..++..| T Consensus 297 EAma~GlPvIa~----------d~~yG~~eiI~~g~nG~Lv~~~d~~~la~~i 339 (372) T cd04949 297 EALSHGLPVISY----------DVNYGPSEIIEDGENGYLVPKGDIEALAEAI 339 (372) T ss_pred HHHHCCCCEEEE----------CCCCCCHHHHCCCCCEEEECCCCHHHHHHHH T ss_conf 999859999980----------5999968884589847996899999999999 No 212 >PRK10419 nikE nickel transporter ATP-binding protein; Provisional Probab=24.57 E-value=39 Score=12.74 Aligned_cols=10 Identities=0% Similarity=-0.273 Sum_probs=6.4 Q ss_pred CCEEEEEEEE Q ss_conf 5406887532 Q gi|254780879|r 424 TDFLETFFSV 433 (652) Q Consensus 424 GD~f~Vlye~ 433 (652) .|++-|+|.. T Consensus 219 adri~Vm~~G 228 (266) T PRK10419 219 CQRVMVMDNG 228 (266) T ss_pred CCEEEEEECC T ss_conf 8989999898 No 213 >cd00728 malate_synt_G Malate synthase G (MSG), monomeric enzyme present in some bacteria. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms to derive their carbon requirements from two-carbon compounds, by bypassing the two carboxylation steps of the citric acid cycle. Probab=24.40 E-value=9.8 Score=16.99 Aligned_cols=23 Identities=30% Similarity=0.505 Sum_probs=10.0 Q ss_pred EECCCEEEEECCCCCCCCCEEEE Q ss_conf 83495899841667888742688 Q gi|254780879|r 575 VKQGQIIGWIGTTGLSTGPHLHY 597 (652) Q Consensus 575 V~qGQvIG~vGsTG~STGPHLHf 597 (652) -+.|---++|=|---+|=--||| T Consensus 523 p~aGAn~AWVPSPTaAtLHA~HY 545 (712) T cd00728 523 PKAGANTAWVPSPTAATLHALHY 545 (712) T ss_pred CCCCCCCCCCCCCHHHHHHHHHH T ss_conf 87876041578927898999888 No 214 >KOG3679 consensus Probab=24.31 E-value=8.7 Score=17.32 Aligned_cols=45 Identities=29% Similarity=0.486 Sum_probs=28.3 Q ss_pred EEEEEEECCEECCCCE-ECCCCCCCCCHHHHHHHHHH----HHHHHHHHH Q ss_conf 6889978678836620-00788787888999999999----999999984 Q gi|254780879|r 595 LHYELIVNGIKVDSTK-VRIPERENLKGDLLQRFAME----KKRINSLLN 639 (652) Q Consensus 595 LHfEv~vnG~~VdP~~-~~lp~~~~l~~~~l~~F~~~----~~~id~ll~ 639 (652) -|||+++||....-+- -|.-.=|.+....|+.|+.. -+.+|.||+ T Consensus 566 hhfelringekleellseravqfraiqrrllarfkdktpaplqhldtlld 615 (802) T KOG3679 566 HHFELRINGEKLEELLSERAVQFRAIQRRLLARFKDKTPAPLQHLDTLLD 615 (802) T ss_pred HEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHC T ss_conf 10477746688999998778899999999998744499861777777752 No 215 >TIGR01172 cysE serine O-acetyltransferase; InterPro: IPR005881 The biosynthesis of L-cysteine is the predominant way by which inorganic sulphur is incorporated into organic compounds. In this process, the most abundant utilizable source of sulphur, inorganic sulphate, is taken up and reduced to sulphide. Sulphide is used to produce L-cysteine, which serves for protein synthesis or the production of other sulphur-containing organic compounds. Two routes for cysteine biosynthesis in nature have been documented. Serine transacetylase (2.3.1.30 from EC) catalyzes steps in pathway I, the activation of L-serine by acetyl-coenzyme A, yielding O-acetyl-L-serine.; GO: 0009001 serine O-acetyltransferase activity, 0006535 cysteine biosynthetic process from serine, 0005737 cytoplasm. Probab=24.28 E-value=40 Score=12.71 Aligned_cols=14 Identities=29% Similarity=0.458 Sum_probs=6.8 Q ss_pred CCCEEEEEEECCCC Q ss_conf 67236889623885 Q gi|254780879|r 443 DSELLYIHARFGET 456 (652) Q Consensus 443 ~geil~A~~~~~g~ 456 (652) +.=.+|=..|++|. T Consensus 92 ddv~iyhGVTLGGt 105 (163) T TIGR01172 92 DDVTIYHGVTLGGT 105 (163) T ss_pred CCEEEEECEEECCC T ss_conf 88378632120678 No 216 >PRK12839 hypothetical protein; Provisional Probab=24.17 E-value=40 Score=12.69 Aligned_cols=24 Identities=8% Similarity=-0.022 Sum_probs=16.1 Q ss_pred CCHHHHHHHHHCCCCHHHHHHHHH Q ss_conf 110256668871999899999999 Q gi|254780879|r 386 IYDGIWRATSFNGMNSNLVKLIMR 409 (652) Q Consensus 386 I~~SLy~aa~~~gip~~ii~~lv~ 409 (652) ..+||-+.|.+.|++.....+-++ T Consensus 428 kadTleELA~~~gid~~~L~~TV~ 451 (574) T PRK12839 428 KGRTIEELAQKCGIDPAGLRATVT 451 (574) T ss_pred ECCCHHHHHHHHCCCHHHHHHHHH T ss_conf 549999999886959899999999 No 217 >PRK09838 periplasmic copper-binding protein; Provisional Probab=24.17 E-value=40 Score=12.69 Aligned_cols=27 Identities=7% Similarity=0.231 Sum_probs=16.7 Q ss_pred CHHHCCCCCEEEEEECCCCCCCEEEEE Q ss_conf 610169988899997278886405899 Q gi|254780879|r 313 RVDQLTKDEILRIGVVQKDDKFTIVRF 339 (652) Q Consensus 313 ~~~~Lr~Gq~L~I~~~~~~~~~~~~r~ 339 (652) .+..|++|+++++.+.+.++...+..+ T Consensus 84 ~l~~lk~Gd~V~F~Fvq~G~~~~l~~I 110 (114) T PRK09838 84 KMSEIKTGDKVAFNFVQQGNLSLLQDI 110 (114) T ss_pred HHHCCCCCCEEEEEEEEECCEEEEEEE T ss_conf 760599999899999963997799998 No 218 >COG1820 NagA N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism] Probab=24.10 E-value=28 Score=13.75 Aligned_cols=11 Identities=18% Similarity=0.102 Sum_probs=4.0 Q ss_pred CEEEEEECCCC Q ss_conf 01368841797 Q gi|254780879|r 275 ADDLIPIQHNT 285 (652) Q Consensus 275 ~e~~v~VK~GD 285 (652) .+.-|+|.-|- T Consensus 183 ~~~giivs~GH 193 (380) T COG1820 183 ANAGIVVSIGH 193 (380) T ss_pred HHCCEEEEECC T ss_conf 86893997157 No 219 >PRK08291 ornithine cyclodeaminase; Validated Probab=24.00 E-value=40 Score=12.67 Aligned_cols=15 Identities=7% Similarity=0.020 Sum_probs=6.8 Q ss_pred CCCCHHHCCCCCEEE Q ss_conf 015610169988899 Q gi|254780879|r 310 NEVRVDQLTKDEILR 324 (652) Q Consensus 310 ~~~~~~~Lr~Gq~L~ 324 (652) ..++...|++|..+. T Consensus 210 Pv~~~~~lkpG~hI~ 224 (330) T PRK08291 210 PILKAEWLHPGLHVT 224 (330) T ss_pred CCCCHHHCCCCCEEE T ss_conf 501510069982899 No 220 >PRK11308 dppF dipeptide transporter ATP-binding subunit; Provisional Probab=23.85 E-value=40 Score=12.65 Aligned_cols=11 Identities=9% Similarity=0.069 Sum_probs=8.0 Q ss_pred CCEEEEEEEEE Q ss_conf 54068875321 Q gi|254780879|r 424 TDFLETFFSVN 434 (652) Q Consensus 424 GD~f~Vlye~~ 434 (652) .|+.-|+|... T Consensus 222 aDri~VMy~G~ 232 (327) T PRK11308 222 ADDVMVMYLGR 232 (327) T ss_pred CCEEEEEECCE T ss_conf 99899998988 No 221 >PRK09099 type III secretion system ATPase; Provisional Probab=23.63 E-value=41 Score=12.62 Aligned_cols=26 Identities=12% Similarity=0.038 Sum_probs=15.5 Q ss_pred CCEEECCCCCCCEEECCCCEEEEEEE Q ss_conf 20030267967279715967999653 Q gi|254780879|r 514 TGVDWAAPRGTPIVAVGDGIVEKANW 539 (652) Q Consensus 514 ~GVD~aAp~GTPI~Aag~G~V~~ag~ 539 (652) .|=|+..|.-+-+++.-||-++-... T Consensus 317 ~~dd~~~pi~d~~~si~DGhivLsr~ 342 (441) T PRK09099 317 EDDSGSDPIAEEVRGILDGHMILSRE 342 (441) T ss_pred CCCCCCCCHHHHHHHHCCEEEEECHH T ss_conf 68877787678777670638998587 No 222 >TIGR01936 nqrA NADH:ubiquinone oxidoreductase, Na(+)-translocating, A subunit; InterPro: IPR008703 This family consists of several bacterial Na^+-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na^+-translocating NADH: ubiquinone oxidoreductase (Na^+-NQR) generates an electrochemical Na^+ potential driven by aerobic respiration .; GO: 0016655 oxidoreductase activity acting on NADH or NADPH quinone or similar compound as acceptor, 0006814 sodium ion transport. Probab=23.53 E-value=25 Score=14.05 Aligned_cols=24 Identities=17% Similarity=0.011 Sum_probs=15.1 Q ss_pred CCCCCCCHHHHHHHHCCCCCCCCC Q ss_conf 444556503344320233322245 Q gi|254780879|r 199 QLDHTAQDEEIKNAIMNQFFLLHN 222 (652) Q Consensus 199 ~~~~~~~~~~~~~~~~~~~~~~~~ 222 (652) ..-.+++.+.+...+-+.+.|..- T Consensus 108 ~~L~~Ls~~~~~~~l~~sGLw~~~ 131 (466) T TIGR01936 108 YDLATLSAEQIKELLLESGLWTAL 131 (466) T ss_pred CCHHHCCHHHHHHHHHHHHHHHHH T ss_conf 460103789999998740057676 No 223 >COG4729 Uncharacterized conserved protein [Function unknown] Probab=23.50 E-value=41 Score=12.61 Aligned_cols=40 Identities=23% Similarity=0.346 Sum_probs=19.8 Q ss_pred CCCEEECCCEEEEECCC-----CCCCCCEEEEEEEECCEECCCCE Q ss_conf 99788349589984166-----78887426889978678836620 Q gi|254780879|r 571 AGTAVKQGQIIGWIGTT-----GLSTGPHLHYELIVNGIKVDSTK 610 (652) Q Consensus 571 ~G~~V~qGQvIG~vGsT-----G~STGPHLHfEv~vnG~~VdP~~ 610 (652) +|..+.-||.++|-+.- -+|++|--||.+-+||+.++-.+ T Consensus 87 ~~~t~~dg~~~~y~~~~~~~~L~~~~s~~~~~~l~vngr~~~l~~ 131 (156) T COG4729 87 EGATLEDGAWFYYRGVRTLQVLRWSRSREAGYRLCVNGRSYALAR 131 (156) T ss_pred CCEEEECCCEEEECCCCCEEEEEEECCCCCCEEEEECCEEEEEEC T ss_conf 855874797798736763346898616645278860887887323 No 224 >PRK13546 teichoic acids export protein ATP-binding subunit; Provisional Probab=23.37 E-value=41 Score=12.59 Aligned_cols=19 Identities=11% Similarity=0.347 Sum_probs=8.4 Q ss_pred HHHHCCCCHHHHHHHHHHH Q ss_conf 9997499989999999985 Q gi|254780879|r 290 AMVHAGYSNGDSAKIAKAL 308 (652) Q Consensus 290 IL~r~Gvs~~ei~~i~~al 308 (652) .+.-.|++..++.+.+..+ T Consensus 109 ~~~~~g~~~~~~~~~~~~~ 127 (264) T PRK13546 109 KMLCMGFKRKEIKAMTPKI 127 (264) T ss_pred HHHHCCCCHHHHHHHHHHH T ss_conf 9987242499999999999 No 225 >TIGR00396 leuS_bact leucyl-tRNA synthetase; InterPro: IPR002302 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Leucyl tRNA synthetase (6.1.1.4 from EC) is an alpha monomer that belongs to class Ia. There are two different families of leucyl-tRNA synthetases. This family includes the eubacterial and mitochondrial synthetases. The crystal structure of leucyl-tRNA synthetase from the hyperthermophile Thermus thermophilus has an overall architecture that is similar to that of isoleucyl-tRNA synthetase, except that the putative editing domain is inserted at a different position in the primary structure. This feature is unique to prokaryote-like leucyl-tRNA synthetases, as is the presence of a novel additional flexibly inserted domain . ; GO: 0000166 nucleotide binding, 0004823 leucine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006429 leucyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=23.29 E-value=37 Score=12.95 Aligned_cols=244 Identities=14% Similarity=0.127 Sum_probs=105.0 Q ss_pred CCCCEEEEEECCCCCHHHHHHH-----CCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEE-ECCCCCCCEEEEEEECCCC Q ss_conf 7640136884179708999997-----499989999999985401561016998889999-7278886405899971688 Q gi|254780879|r 272 PEFADDLIPIQHNTTIFDAMVH-----AGYSNGDSAKIAKALKNEVRVDQLTKDEILRIG-VVQKDDKFTIVRFSIYHKQ 345 (652) Q Consensus 272 ~~~~e~~v~VK~GDTL~~IL~r-----~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~-~~~~~~~~~~~r~si~~~~ 345 (652) ..+.++.+.+.+-.+...+|.+ .|+...++.+.+...-...+..+-+.-=+||=. +++. |+ =|. T Consensus 390 ~A~t~~g~~~ns~tstdGvltkeC~~f~Gl~~~~A~~~I~~~L~~~~~gk~~v~YrLRDW~~SRQ-------RY---WG~ 459 (916) T TIGR00396 390 QAYTEDGVLVNSSTSTDGVLTKECGEFNGLNSSEAKEAIIKMLEKEGKGKRKVNYRLRDWLFSRQ-------RY---WGE 459 (916) T ss_pred HHHHHCCCEECCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCEEEEEEEECCCEEEE-------CC---CCC T ss_conf 76764652216876534410100022237761789999999998638850212346532534400-------02---688 Q ss_pred CEEEEEEECCCCCEEECCCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHCCCCC Q ss_conf 34899984278843201333210000012211123345421102566688719998999999997301110121014454 Q gi|254780879|r 346 KHLLTIALNDNNEYVLGVEPVKMDINHQMDYMRTSEESPNIYDGIWRATSFNGMNSNLVKLIMRTLASSVNLQEHLKPTD 425 (652) Q Consensus 346 ~~~~~va~~d~g~fv~~~ep~~~~~~~~~~~~~~~~~~~~I~~SLy~aa~~~gip~~ii~~lv~i~a~dVDFqr~ir~GD 425 (652) ..- +--.+.|..++..+ -.....-++.......|++.+ |-.-+.+-+++-.-...+. ..|..| T Consensus 460 PIP--iih~e~g~~~P~~~---~dLPv~LP~~~~~~~~G~~~s-----------PL~~~~~W~~v~~~~~~~~-A~RETd 522 (916) T TIGR00396 460 PIP--IIHCEDGGAVPVPE---EDLPVKLPELVNYDGSGTGES-----------PLSRIKEWVNVTCPSCGKP-ALRETD 522 (916) T ss_pred CCC--EEEECCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCC-----------HHHHCCCCEEECCCCCCCC-CCCCCC T ss_conf 987--78806768424434---468710750023578889888-----------0430746324147887987-543378 Q ss_pred EEEEEEE---------EEC-CC-----CCCCCC---CCEEEEEEECCCCCCC-----CCCCCCCCCCCCCCCCCCCCCH- Q ss_conf 0688753---------211-57-----851246---7236889623885420-----1345576655444335566100- Q gi|254780879|r 426 FLETFFS---------VNH-AN-----NQASDD---SELLYIHARFGETRTR-----FYRFLNPVDGSVEYFNENGKSS- 481 (652) Q Consensus 426 ~f~Vlye---------~~~-~~-----g~~~~~---geil~A~~~~~g~~~~-----~yrf~~~~~~~~~yyd~~G~S~- 481 (652) ++.-+.+ ..- .. .+..+. ..=|.+.++.||-++- |.||-++--. |..--+. T Consensus 523 TMdtf~~SsWYylRY~~p~~n~~FWPi~~~~d~e~~~~wlPVD~YiGG~EHAiLHLLY~RF~hK~L~-----D~g~v~~P 597 (916) T TIGR00396 523 TMDTFIGSSWYYLRYLDPKNNTNFWPIDQPFDKEKAEYWLPVDLYIGGIEHAILHLLYARFFHKFLY-----DLGLVSTP 597 (916) T ss_pred CCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHH-----HCCCCCCC T ss_conf 7630577789998603500176668732130278897558844102626899899888899999997-----45761587 Q ss_pred --HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCC-EEEE Q ss_conf --0001123334541023567641434044346420030267967279715967999653089700799983997-4882 Q gi|254780879|r 482 --RPFLLRTPVPFGRMTSGFGMRYHPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNG-YVSS 558 (652) Q Consensus 482 --~k~llr~Pv~~~risS~Fg~R~hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~G-y~T~ 558 (652) -+-.+.+-+.-|-|.+ +|.-|..|.|--+.-.=.-.|+. +.+.+-++-+.+..++. ..+. T Consensus 598 aGi~EPFkKL~~QGMVlg----------------~~f~y~~~~g~~~W~~p~d~~~~-~d~~~d~~~~~d~~~~~~~~~~ 660 (916) T TIGR00396 598 AGIKEPFKKLINQGMVLG----------------DAFYYKKPNGKRIWVVPADELIE-RDEKGDIKKAKDKSGGELVVVG 660 (916) T ss_pred CCCCCHHHHHHHCCEEEC----------------CCEEECCCCCCEEEEECCCCEEE-CCCCCCCCCCEECCCCCEEEEE T ss_conf 766571455420000211----------------61341389973677645751661-0466786542325888247887 Q ss_pred EHHHHH Q ss_conf 002144 Q gi|254780879|r 559 YNHQDA 564 (652) Q Consensus 559 YaHlS~ 564 (652) |+=||+ T Consensus 661 ~~KMSK 666 (916) T TIGR00396 661 YEKMSK 666 (916) T ss_pred EEEECC T ss_conf 776202 No 226 >TIGR00986 3a0801s05tom22 mitochondrial import receptor subunit; InterPro: IPR005683 The mitochondrial protein translocase (MPT) family, which brings nuclearly encoded preproteins into mitochondria, is very complex with 19 currently identified protein constituents. These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins.The inner membrane translocase is formed of a complex with a number of proteins, including the Tim17, Tim23 and Tim44 subunits. This family is specific for the Tom22 proteins. ; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0006886 intracellular protein transport, 0005741 mitochondrial outer membrane. Probab=23.26 E-value=39 Score=12.75 Aligned_cols=25 Identities=24% Similarity=0.328 Sum_probs=16.9 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 9999999999876268841004862 Q gi|254780879|r 52 TSGVIIGGSLLTALDGHQKIAIPAK 76 (652) Q Consensus 52 ~~~~l~g~a~~~aldg~~~~a~p~~ 76 (652) |+++|||+=+..||..+++++.-++ T Consensus 104 tsaLLlGVPf~~s~~eeq~l~emEk 128 (152) T TIGR00986 104 TSALLLGVPFALSLAEEQQLIEMEK 128 (152) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9899988899999998768999988 No 227 >COG4172 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only] Probab=23.18 E-value=41 Score=12.57 Aligned_cols=19 Identities=26% Similarity=0.665 Sum_probs=14.8 Q ss_pred CCCEEECCCEEEEECCCCC Q ss_conf 9978834958998416678 Q gi|254780879|r 571 AGTAVKQGQIIGWIGTTGL 589 (652) Q Consensus 571 ~G~~V~qGQvIG~vGsTG~ 589 (652) ..-..++||.+|.||-+|. T Consensus 306 isl~L~~gqTlGlVGESGS 324 (534) T COG4172 306 ISLTLRRGQTLGLVGESGS 324 (534) T ss_pred CEEEECCCCEEEEEECCCC T ss_conf 4367538976777705889 No 228 >cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold. Probab=23.13 E-value=42 Score=12.56 Aligned_cols=45 Identities=16% Similarity=0.217 Sum_probs=26.3 Q ss_pred CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHC--CCCCCEEECCCEE Q ss_conf 96799965308970079998399748820021445411--8899788349589 Q gi|254780879|r 531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKN--IKAGTAVKQGQII 581 (652) Q Consensus 531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~g--V~~G~~V~qGQvI 581 (652) .|+|...- .||-+|.+. +..+.+.|.|.+... ..+-..++.||.| T Consensus 2 ~G~V~~i~---~~G~fV~~~---~~~~gli~~s~~s~~~~~~~~~~~~~G~~V 48 (65) T cd00164 2 TGKVVSIT---KFGVFVELE---DGVEGLVHISELSDKFVKDPSEVFKVGDEV 48 (65) T ss_pred EEEEEEEE---CCEEEEEEC---CCEEEEEEHHHHCCCCCCCHHHEECCCCEE T ss_conf 89999997---845999989---871788988891676535951098599999 No 229 >pfam04239 DUF421 Protein of unknown function (DUF421). YDFR family Probab=23.05 E-value=42 Score=12.55 Aligned_cols=40 Identities=8% Similarity=0.155 Sum_probs=31.7 Q ss_pred EEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCC Q ss_conf 68841797089999974999899999999854015610169 Q gi|254780879|r 278 LIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLT 318 (652) Q Consensus 278 ~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr 318 (652) ++.|+.|.-+...+++.+++.+|+...+.. ++.+++..++ T Consensus 9 ~~li~~G~i~~~~l~k~~it~~dl~~~LR~-~gi~~~~~V~ 48 (98) T pfam04239 9 TLLIENGKILEENLKKERLTEDDLLSALRE-KGIFDLSDVE 48 (98) T ss_pred EEEEECCEECHHHHHHCCCCHHHHHHHHHH-CCCCCHHHHC T ss_conf 799999999699998849999999999998-3999988902 No 230 >TIGR02465 chlorocat_1_2 chlorocatechol 1,2-dioxygenase; InterPro: IPR012817 Members of this protein family are chlorocatechol 1,2-dioxygenase. This protein is closely related to catechol 1,2-dioxygenase, IPR012801 from INTERPRO, 1.13.11.1 from EC. Note: a number of annotated database entries for members of this family have EC numbers that refers to IPR012801 from INTERPRO; whereas members of this family acts in pathways for the biodegradation of chlorinated aromatic compounds.; GO: 0005506 iron ion binding, 0018575 chlorocatechol 12-dioxygenase activity, 0006725 aromatic compound metabolic process. Probab=23.03 E-value=40 Score=12.67 Aligned_cols=26 Identities=12% Similarity=0.106 Sum_probs=14.1 Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHCCC Q ss_conf 89999974999899999999854015 Q gi|254780879|r 287 IFDAMVHAGYSNGDSAKIAKALKNEV 312 (652) Q Consensus 287 L~~IL~r~Gvs~~ei~~i~~al~~~~ 312 (652) +-++|.+.-|+.+|=..++.-|-+.. T Consensus 15 vR~~L~~heVT~~EYr~g~~Yl~~v~ 40 (258) T TIGR02465 15 VRDVLVRHEVTEDEYRTGVQYLMKVA 40 (258) T ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHH T ss_conf 99987406688478999999988643 No 231 >pfam08724 Rep_N Rep protein catalytic domain like. Adeno-associated virus (AAV) Replication (Rep) protein is essential for viral replication and integration. The catalytic domain has DNA binding and endonuclease activity. Probab=22.94 E-value=42 Score=12.54 Aligned_cols=11 Identities=9% Similarity=0.075 Sum_probs=4.7 Q ss_pred EEEEECCCCCH Q ss_conf 36884179708 Q gi|254780879|r 277 DLIPIQHNTTI 287 (652) Q Consensus 277 ~~v~VK~GDTL 287 (652) -+|++-.|..+ T Consensus 86 HlHvlI~~~gv 96 (186) T pfam08724 86 HLHVLIGGPGV 96 (186) T ss_pred EEEEEECCCCC T ss_conf 79999648997 No 232 >PRK03695 vitamin B12-transporter ATPase; Provisional Probab=22.54 E-value=43 Score=12.48 Aligned_cols=22 Identities=5% Similarity=0.030 Sum_probs=8.9 Q ss_pred ECCCCCCCEEECCCCEEEEEEE Q ss_conf 0267967279715967999653 Q gi|254780879|r 518 WAAPRGTPIVAVGDGIVEKANW 539 (652) Q Consensus 518 ~aAp~GTPI~Aag~G~V~~ag~ 539 (652) ++...-.-|+--.+|.|+..|- T Consensus 192 ~~~~~~dri~vl~~G~iv~~G~ 213 (245) T PRK03695 192 HTLRHADRVWLLKQGKLLASGR 213 (245) T ss_pred HHHHHCCEEEEEECCEEEEEEC T ss_conf 9999799999998998999907 No 233 >pfam08986 DUF1889 Domain of unknown function (DUF1889). This domain is found in a set of hypothetical bacterial proteins. Probab=22.29 E-value=13 Score=16.07 Aligned_cols=17 Identities=29% Similarity=0.634 Sum_probs=6.8 Q ss_pred CCEEEEECCCCEEEEEHH Q ss_conf 007999839974882002 Q gi|254780879|r 544 GKQTLIHHGNGYVSSYNH 561 (652) Q Consensus 544 Gn~V~I~H~~Gy~T~YaH 561 (652) |+.|+|+|. .|-+.|.| T Consensus 96 GerivIKnP-EyFstYM~ 112 (119) T pfam08986 96 GERIVIKNP-EYFSTYMQ 112 (119) T ss_pred CCEEEECCH-HHHHHHHH T ss_conf 774775495-89999999 No 234 >TIGR02441 fa_ox_alpha_mit fatty acid oxidation complex, alpha subunit, mitochondrial; InterPro: IPR012803 Members of this family represent the alpha subunit of the mitochondrial multifunctional fatty acid degradation enzyme complex. Subunit activities include: enoyl-CoA hydratase (4.2.1.17 from EC) and 3-hydroxyacyl-CoA dehydrogenase (1.1.1.35 from EC). Some characterization of these proteins has been done in human (P40939 from SWISSPROT), pig (Q29554 from SWISSPROT) and rat (Q64428 from SWISSPROT). The beta subunit has acetyl-CoA C-acyltransferase (2.3.1.16 from EC) activity.; GO: 0003857 3-hydroxyacyl-CoA dehydrogenase activity, 0004300 enoyl-CoA hydratase activity, 0006635 fatty acid beta-oxidation, 0005739 mitochondrion, 0016507 fatty acid beta-oxidation multienzyme complex. Probab=22.27 E-value=43 Score=12.44 Aligned_cols=34 Identities=26% Similarity=0.427 Sum_probs=18.0 Q ss_pred CCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 35566100000112333454102356764143404 Q gi|254780879|r 474 FNENGKSSRPFLLRTPVPFGRMTSGFGMRYHPILG 508 (652) Q Consensus 474 yd~~G~S~~k~llr~Pv~~~risS~Fg~R~hPilg 508 (652) -+|----+.-..|-.|..+ -|.|-||.-.=|.+| T Consensus 659 vNEA~lCL~EgiL~~P~eG-DigaVFGlGFPPf~G 692 (740) T TIGR02441 659 VNEAVLCLEEGILASPLEG-DIGAVFGLGFPPFLG 692 (740) T ss_pred HHHHHHHHHCCCCCCCCCC-CEEEECCCCCCCCCC T ss_conf 8999986303423778887-616662667888885 No 235 >TIGR02645 ARCH_P_rylase putative thymidine phosphorylase; InterPro: IPR013466 Proteins in this entry are closely related to characterised examples of thymidine phosphorylase (2.4.2.4 from EC) and pyrimidine nucleoside phosphorylase (2.4.2.2 from EC). Most examples are found in the archaea, but other examples are found in bacteria such as Legionella pneumophila (strain Paris) and Rhodopseudomonas palustris CGA009.; GO: 0009032 thymidine phosphorylase activity. Probab=22.19 E-value=34 Score=13.20 Aligned_cols=24 Identities=8% Similarity=0.178 Sum_probs=20.1 Q ss_pred HHHHHCCCCHHHHHHHHHHHHCCC Q ss_conf 999974999899999999854015 Q gi|254780879|r 289 DAMVHAGYSNGDSAKIAKALKNEV 312 (652) Q Consensus 289 ~IL~r~Gvs~~ei~~i~~al~~~~ 312 (652) .+|.|-.++.+|+.+|++..++-. T Consensus 212 EVLtrV~ls~~E~K~iV~~~ggcL 235 (499) T TIGR02645 212 EVLTRVELSVEEIKRIVEKVGGCL 235 (499) T ss_pred EEECCCCCCHHHHHHHHHHCCCEE T ss_conf 672165224788989986408645 No 236 >cd00187 TOP4c DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA topology by catalysing the concerted breakage and rejoining of DNA strands during normal cellular growth. Probab=22.06 E-value=35 Score=13.10 Aligned_cols=32 Identities=6% Similarity=0.043 Sum_probs=21.4 Q ss_pred EECCCEEEEECCCCCCCCCCCCCCCCHHHHHC Q ss_conf 64571002100236553335897987125522 Q gi|254780879|r 130 KKIPFAYARMTFATPYPKVKDHPKFDPLKIFS 161 (652) Q Consensus 130 ~~~pf~~~~~~l~~~~~~~~~~p~f~p~~~~~ 161 (652) -.-|.+.|+.+-.-..+.+..||||||.-+.. T Consensus 132 p~iP~iLvNGa~GIgtG~sT~IP~hNp~eii~ 163 (445) T cd00187 132 PIFPNLLVNGSSGIAVGMATNIPPHNLREVID 163 (445) T ss_pred CCCHHHHHCCCEEEEEEECCCCCCCCHHHHHH T ss_conf 43307763466133420005678878899999 No 237 >PRK04722 consensus Probab=22.05 E-value=44 Score=12.41 Aligned_cols=33 Identities=6% Similarity=0.007 Sum_probs=20.1 Q ss_pred HHHHHCCCCHHHHHH----HHHHHHCCCCHHHCCCCCE Q ss_conf 999974999899999----9998540156101699888 Q gi|254780879|r 289 DAMVHAGYSNGDSAK----IAKALKNEVRVDQLTKDEI 322 (652) Q Consensus 289 ~IL~r~Gvs~~ei~~----i~~al~~~~~~~~Lr~Gq~ 322 (652) .-.+.|+++-+|+.. --.+++..+ .++|++|-+ T Consensus 38 ~f~~~y~idm~Ea~~~~~~~Y~sfn~FF-tR~Lk~~~R 74 (280) T PRK04722 38 TVTRKFGVDLSEAQEPDPRAYPTFNAFF-TRALKPGAR 74 (280) T ss_pred HHHHHHCCCHHHHCCCCHHHCCCHHHHE-EECCCCCCC T ss_conf 9999979797897378823378788846-220577888 No 238 >PRK03598 hypothetical protein; Provisional Probab=21.78 E-value=44 Score=12.38 Aligned_cols=14 Identities=7% Similarity=0.145 Sum_probs=7.7 Q ss_pred HHCCCCCEEEEEEE Q ss_conf 10144540688753 Q gi|254780879|r 419 EHLKPTDFLETFFS 432 (652) Q Consensus 419 r~ir~GD~f~Vlye 432 (652) ..+++|+..+|... T Consensus 252 ~~v~~Gq~v~i~~d 265 (331) T PRK03598 252 GQAQPGRKVLVYTD 265 (331) T ss_pred HHCCCCCEEEEEEE T ss_conf 52889998999994 No 239 >cd03795 GT1_like_4 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP-linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homolog Probab=21.41 E-value=38 Score=12.81 Aligned_cols=29 Identities=24% Similarity=0.226 Sum_probs=15.6 Q ss_pred CCCCCCCEEECCCC-EEEEEEEECCCCCEE Q ss_conf 26796727971596-799965308970079 Q gi|254780879|r 519 AAPRGTPIVAVGDG-IVEKANWAGGYGKQT 547 (652) Q Consensus 519 aAp~GTPI~Aag~G-~V~~ag~~~GyGn~V 547 (652) |..+|+||+|+.-| -....-.++..|.++ T Consensus 285 Ama~G~PVVat~~gg~~~~i~~~~~~G~l~ 314 (357) T cd03795 285 AMAFGKPVISTEIGTGGSYVNLHGVTGLVV 314 (357) T ss_pred HHHCCCCEEEECCCCCHHHHEECCCEEEEE T ss_conf 998799899935999815605569579997 No 240 >cd03689 RF3_II RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the ribosome after release of the nascent polypeptide. RF3 in the GDP state binds to the ribosomal class I RF complex, followed by an exchange of GDP for GTP and release of the class I RF. Sequence comparison of class II release factors with elongation factors shows that prokaryotic RF3 is more similar to EF-G whereas eukaryotic eRF3 is more similar to eEF1A, implying that their precise function may differ. Probab=21.23 E-value=45 Score=12.30 Aligned_cols=24 Identities=25% Similarity=0.418 Sum_probs=17.4 Q ss_pred CCEEECCCEEEEECCCCCCCCCEE Q ss_conf 978834958998416678887426 Q gi|254780879|r 572 GTAVKQGQIIGWIGTTGLSTGPHL 595 (652) Q Consensus 572 G~~V~qGQvIG~vGsTG~STGPHL 595 (652) =+....|+|||.+|.-...||--| T Consensus 59 ie~A~aGDIvav~g~~~~~tGDTL 82 (85) T cd03689 59 VDEAYPGDIIGLVNPGNFQIGDTL 82 (85) T ss_pred ECEEECCCEEEEECCCCCEECCCC T ss_conf 034938989998279987314651 No 241 >pfam05775 AfaD Enterobacteria AfaD invasin protein. This family consists of several AfaD and related proteins from Escherichia coli and Salmonella bacteria. The afa gene clusters encode an afimbrial adhesive sheath produced by Escherichia coli. The adhesive sheath is composed of two proteins, AfaD and AfaE, which are independently exposed at the bacterial cell surface. AfaE is required for bacterial adhesion to HeLa cells and AfaD for the uptake of adherent bacteria into these cells. Probab=21.22 E-value=45 Score=12.30 Aligned_cols=10 Identities=30% Similarity=0.219 Sum_probs=5.1 Q ss_pred HHCCCCCEEE Q ss_conf 0169988899 Q gi|254780879|r 315 DQLTKDEILR 324 (652) Q Consensus 315 ~~Lr~Gq~L~ 324 (652) ..|+.|++|- T Consensus 31 ~~lrDG~~ia 40 (136) T pfam05775 31 GQLRDGMKLA 40 (136) T ss_pred CCCCCCCEEE T ss_conf 4234773887 No 242 >PRK13635 cbiO cobalt transporter ATP-binding subunit; Provisional Probab=21.21 E-value=45 Score=12.30 Aligned_cols=14 Identities=7% Similarity=0.166 Sum_probs=6.6 Q ss_pred HHHCCCCHHHHHHH Q ss_conf 99749998999999 Q gi|254780879|r 291 MVHAGYSNGDSAKI 304 (652) Q Consensus 291 L~r~Gvs~~ei~~i 304 (652) ++..|++.+++.+. T Consensus 107 l~~~g~~~~e~~~r 120 (279) T PRK13635 107 LENIGVPREEMVER 120 (279) T ss_pred HHHCCCCHHHHHHH T ss_conf 98779999999999 No 243 >PRK11288 araG L-arabinose transporter ATP-binding protein; Provisional Probab=21.18 E-value=45 Score=12.30 Aligned_cols=15 Identities=47% Similarity=1.077 Sum_probs=7.6 Q ss_pred EEECCCEEEEECCCC Q ss_conf 883495899841667 Q gi|254780879|r 574 AVKQGQIIGWIGTTG 588 (652) Q Consensus 574 ~V~qGQvIG~vGsTG 588 (652) .|++|+++|.+|-.| T Consensus 275 ~v~~GEivgivG~nG 289 (501) T PRK11288 275 AVRRGEIVGFFGLVG 289 (501) T ss_pred EEECCEEEEEECCCC T ss_conf 870883999756888 No 244 >PRK13633 cobalt transporter ATP-binding subunit; Provisional Probab=21.13 E-value=45 Score=12.29 Aligned_cols=25 Identities=8% Similarity=0.033 Sum_probs=12.2 Q ss_pred HHHHCCCCHHHHHHHHHHHHCCCCH Q ss_conf 9997499989999999985401561 Q gi|254780879|r 290 AMVHAGYSNGDSAKIAKALKNEVRV 314 (652) Q Consensus 290 IL~r~Gvs~~ei~~i~~al~~~~~~ 314 (652) -++..|++.+++.+-+...-....+ T Consensus 111 g~~~~g~~~~e~~~rv~~~l~~~gL 135 (281) T PRK13633 111 GPENLGIPPEEIRERVDESLKKVGM 135 (281) T ss_pred HHHHCCCCHHHHHHHHHHHHHHCCC T ss_conf 8988699999999999999986794 No 245 >cd03248 ABCC_TAP TAP, the Transporter Associated with Antigen Processing; TAP is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on major histocompatibility complex (MHC) I molecules. Loaded MHC I leave the ER and display their antigenic cargo on the cell surface to cytotoxic T cells. Subsequently, virus-infected or malignantly transformed cells can be eliminated. TAP belongs to the large family of ATP-binding cassette (ABC) transporters, which translocate a vast variety of solutes across membranes. Probab=21.08 E-value=45 Score=12.28 Aligned_cols=29 Identities=7% Similarity=0.060 Sum_probs=11.9 Q ss_pred CCEEEEEECCCCCHHHHHHHCCCCHHHHHH Q ss_conf 401368841797089999974999899999 Q gi|254780879|r 274 FADDLIPIQHNTTIFDAMVHAGYSNGDSAK 303 (652) Q Consensus 274 ~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~ 303 (652) ...-...|++|+.+. |.-..|--...+.+ T Consensus 30 L~~is~~i~~Ge~va-IvG~sGsGKSTL~~ 58 (226) T cd03248 30 LQDVSFTLHPGEVTA-LVGPSGSGKSTVVA 58 (226) T ss_pred EECEEEEECCCCEEE-EECCCCCHHHHHHH T ss_conf 745389982999999-99999984999999 No 246 >cd03257 ABC_NikE_OppD_transporters The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and NikC), and two ATPase (NikD and NikE). The NikABCDE transporter is synthesized under anaerobic conditions to meet the increased demand for nickel resulting from hydrogenase synthesis. The molecular mechanism of nickel uptake in many bacteria and most archaea is not known. Many other members of this ABC family are also involved in the uptake of dipeptides and oligopeptides. The oligopeptide transport system (Opp) is a five-component ABC transport composed of a membrane-anchored substrate binding proteins (SRP), OppA, two transmembrane proteins, OppB and OppC, and two ATP-binding domains, OppD and OppF. Probab=21.01 E-value=46 Score=12.27 Aligned_cols=25 Identities=16% Similarity=0.272 Sum_probs=12.1 Q ss_pred EEECCCCCHHHHHHHCCCCHHHHHHH Q ss_conf 88417970899999749998999999 Q gi|254780879|r 279 IPIQHNTTIFDAMVHAGYSNGDSAKI 304 (652) Q Consensus 279 v~VK~GDTL~~IL~r~Gvs~~ei~~i 304 (652) ..|++|+.+ .|+-..|.-.....++ T Consensus 26 l~i~~Ge~~-~iiG~sGsGKSTLl~~ 50 (228) T cd03257 26 FSIKKGETL-GLVGESGSGKSTLARA 50 (228) T ss_pred EEECCCCEE-EEECCCCCHHHHHHHH T ss_conf 898699899-9999999869999999 No 247 >TIGR00848 fruA PTS system, fructose subfamily, IIA component; InterPro: IPR004715 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) , is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC . These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose , , , . The Man family is unique in several respects among PTS permease families. It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The PTS Fructose-Mannitol (Fru) family is a large and complex family which includes several sequenced fructose and mannitol-specific permeases as well as several putative PTS permeases of unknown specificities. The fructose permeases of this family phosphorylate fructose on the 1-position. Those of family 4.6 phosphorylate fructose on the 6-position. The Fru family PTS systems typically have 3 domains, IIA, IIB and IIC, which may be found as 1 or more proteins. The fructose and mannitol transporters form separate phylogenetic clusters in this family. This family is specific for the IIA domain of the fructose PTS transporters. Also similar to the Enzyme IIA Fru subunits of the PTS is Enzyme IIA Ntr (nitrogen) found in Escherichia coli and other organisms, which may play a solely regulatory role. ; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016021 integral to membrane. Probab=20.88 E-value=38 Score=12.84 Aligned_cols=43 Identities=9% Similarity=0.135 Sum_probs=18.1 Q ss_pred CHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECC Q ss_conf 08999997499989999999985401561016998889999727 Q gi|254780879|r 286 TIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQ 329 (652) Q Consensus 286 TL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~ 329 (652) .|+..|...|+-.+ ..+..+.+..+=....--.|+-+-|+-.+ T Consensus 23 ~La~~l~~~G~~~d-~~~f~~~~~~RE~~~~TG~g~gvAiPH~k 65 (133) T TIGR00848 23 FLANKLLENGYISD-KEEFLEDLLKREEEGTTGIGDGVAIPHAK 65 (133) T ss_pred HHHHHHHHCCCCCC-HHHHHHHHHHHHHCCCCCCCCCCCCCCCC T ss_conf 99999984465378-89999999988630588664441045332 No 248 >COG3767 Uncharacterized low-complexity protein [Function unknown] Probab=20.63 E-value=46 Score=12.22 Aligned_cols=30 Identities=17% Similarity=0.310 Sum_probs=23.6 Q ss_pred HHHHHHHHHHHHHHHHHH-HHCCCCCCCCCC Q ss_conf 899999999999999987-626884100486 Q gi|254780879|r 46 TFFAGITSGVIIGGSLLT-ALDGHQKIAIPA 75 (652) Q Consensus 46 t~ltg~~~~~l~g~a~~~-aldg~~~~a~p~ 75 (652) .+++-++|++|||.+.-+ ++.+...|++-+ T Consensus 5 ~~~~alagA~~l~~a~~~~a~~~~~~fav~~ 35 (95) T COG3767 5 ATAAALAGALLLGAAAVAQAENKSASFAVGA 35 (95) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC T ss_conf 8899998789999888889872678553333 No 249 >PRK13636 cbiO cobalt transporter ATP-binding subunit; Provisional Probab=20.62 E-value=46 Score=12.22 Aligned_cols=10 Identities=10% Similarity=0.116 Sum_probs=3.6 Q ss_pred CCCCHHHHHH Q ss_conf 4999899999 Q gi|254780879|r 294 AGYSNGDSAK 303 (652) Q Consensus 294 ~Gvs~~ei~~ 303 (652) .|++.+++.+ T Consensus 111 ~g~~~~e~~~ 120 (285) T PRK13636 111 LKLPEDEVRK 120 (285) T ss_pred CCCCHHHHHH T ss_conf 5999999999 No 250 >TIGR00078 nadC nicotinate-nucleotide pyrophosphorylase; InterPro: IPR004393 Nicotinate-nucleotide pyrophosphorylase (2.4.2.19 from EC), also known as quinolinate phosphoribosyltransferase (decarboxylating), catalyses the conversion of nicotinate D-ribonucleotide, pyrophosphate and carbon dioxide into pyridine-2,3-dicarboxylate and 5-phospho-alpha-D-ribose 1-diphosphate. This enzyme is a type II phosphoribosyltransferase which provides the de novo source of nicotinate mononucleotide (NAMN) for NAD biosynthesis in both prokaryotes and eukaryotes , . Structural studies have shown that the active form of this enzyme is a homodimer with an unsual fold , , . The N-terminal forms a mixed alpha/beta domain, while the C-terminal region forms a multi-stranded, open alpha/beta barrel. The active site is found at the C-terminal ends of the beta strands of the alpha/beta barrel, and is bordered by the N-terminal domain of the second subunit of the dimer. It contains several conserved charged residues thought to be important determinants of substrate binding and catalysis. ; GO: 0004514 nicotinate-nucleotide diphosphorylase (carboxylating) activity, 0019363 pyridine nucleotide biosynthetic process. Probab=20.62 E-value=46 Score=12.22 Aligned_cols=13 Identities=23% Similarity=0.327 Sum_probs=5.7 Q ss_pred HHHHHHHHHHHCC Q ss_conf 9999999985401 Q gi|254780879|r 299 GDSAKIAKALKNE 311 (652) Q Consensus 299 ~ei~~i~~al~~~ 311 (652) ...+++++++++. T Consensus 107 T~Tr~~v~~~~~~ 119 (276) T TIGR00078 107 TATRKYVEALRGT 119 (276) T ss_pred HHHHHHHHHHHCC T ss_conf 9999999998458 No 251 >PRK13642 cbiO cobalt transporter ATP-binding subunit; Provisional Probab=20.24 E-value=47 Score=12.16 Aligned_cols=15 Identities=20% Similarity=0.237 Sum_probs=7.7 Q ss_pred HHHCCCCHHHHHHHH Q ss_conf 997499989999999 Q gi|254780879|r 291 MVHAGYSNGDSAKIA 305 (652) Q Consensus 291 L~r~Gvs~~ei~~i~ 305 (652) ++..|++.+++.+.+ T Consensus 107 ~~~~~~~~~e~~~~v 121 (277) T PRK13642 107 MENQGIPREEMIKRV 121 (277) T ss_pred HHHCCCCHHHHHHHH T ss_conf 766699999999999 No 252 >PRK12837 3-ketosteroid-delta-1-dehydrogenase; Provisional Probab=20.16 E-value=47 Score=12.15 Aligned_cols=24 Identities=8% Similarity=0.066 Sum_probs=16.1 Q ss_pred CCHHHHHHHHHCCCCHHHHHHHHH Q ss_conf 110256668871999899999999 Q gi|254780879|r 386 IYDGIWRATSFNGMNSNLVKLIMR 409 (652) Q Consensus 386 I~~SLy~aa~~~gip~~ii~~lv~ 409 (652) ..++|-+.|.+.|+|.....+-+. T Consensus 376 ~adTleeLA~~~gi~~~~L~~Tv~ 399 (515) T PRK12837 376 TADTLEELAAKIGVPADALTATVA 399 (515) T ss_pred ECCCHHHHHHHHCCCHHHHHHHHH T ss_conf 459899999986959999999999 No 253 >PRK05659 sulfur carrier protein ThiS; Validated Probab=20.08 E-value=24 Score=14.20 Aligned_cols=46 Identities=9% Similarity=0.190 Sum_probs=30.3 Q ss_pred EEEECCCCCHHHHHHHCCCCHHHHHHHHHHH------HCCCCHHHCCCCCEEEEE Q ss_conf 6884179708999997499989999999985------401561016998889999 Q gi|254780879|r 278 LIPIQHNTTIFDAMVHAGYSNGDSAKIAKAL------KNEVRVDQLTKDEILRIG 326 (652) Q Consensus 278 ~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al------~~~~~~~~Lr~Gq~L~I~ 326 (652) ...+..+-||.++|...++...-++ -++ +..+....|+.|+++.|. T Consensus 9 ~~~~~~~~tl~~Ll~~l~~~~~~vA---VevN~~ivpr~~~~~~~L~egD~iEIv 60 (66) T PRK05659 9 PRELPDGESVAALLAREGLAGRRVA---VEVNGEIVPRSQHASTALREGDVVEIV 60 (66) T ss_pred EEECCCCCCHHHHHHHCCCCCCCEE---EEECCEECCHHHHCCCCCCCCCEEEEE T ss_conf 8786999969999987699998099---998998817789572658999999999 Done!